Full data view for gene B3GALT6

Ehlers Danlos Syndrome Variant Database


Information The variants shown are described using the NM_080605.3 transcript reference sequence.

101 entries on 2 pages. Showing entries 1 - 100.
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Effect     
Exon     
AscendingDNA change (cDNA)     
RNA change     
Protein     
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Type/DNA     
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Clinical classification     
DNA change (genomic) (hg19)     
DNA change (hg38)     
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Variant remarks     
Reference     
ClinVar ID     
dbSNP ID     
Origin     
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Frequency     
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VIP     
Methylation     
Template     
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Disease     
ID_report     
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?/. - c.-3575_-3573del r.(?) p.(=) - - Unknown - VUS g.1164084_1164086del g.1228704_1228706del SDF4(NM_016176.3):c.90_92del (p.(Leu31del)) - B3GALT6_000052 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/+? 1 c.1A>G r.(?) p.0? initiating methionine substitution Parent #1 - likely pathogenic g.1167659A>G - - - B3GALT6_000028 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 Patient 1 PubMed: Nakajima et al., 2013 The patient had a sibling who was also compound heterozygous for both variants and had a similar phenotype.c.1A>G showed a decreased molecular weight ~4kD lower compared to the WT protein. The authors suggested that the translation initiation at the second ATG of the coding sequence (position c.124) would become the initiation codon, resulting in a protein change of p.Met1_Ala41del.The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.1A>G r.(?) p.0? initiating methionine substitution Parent #1 - likely pathogenic g.1167659A>G - - - B3GALT6_000028 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 Patient 3 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would cause a 41 amino acid deletion due to the second ATG becoming the initiating codon. The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.1A>G r.(?) p.0? initiating methionine substitution Unknown - likely pathogenic g.1167659A>G - - - B3GALT6_000028 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - SEMDJL1 P4 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would result in a 41aa deletion due to the second ATG being the initiation codon. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.1A>G r.(?) p.0? initiating methionine substitution Parent #1 - likely pathogenic g.1167659A>G - - - B3GALT6_000028 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 P5 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would result in a 41 aa deletion due to the second ATG becoming the initiating codon. The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.1A>G r.(?) p.0? initiating methionine substitution Parent #1 - likely pathogenic g.1167659A>G - - - B3GALT6_000028 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 P7 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would result in a 41aa deletion due to the second ATG becoming the initiating codon. The technique used was whole exome sequencing. - - Japan;Singapore Japanese/Singaporean - - - - 1 Raymond Dalgleish
+/+ 1 c.3G>A r.(?) p.0? initiating methionine substitution Unknown - pathogenic g.1167661G>A - - - B3GALT6_000016 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - India Indian - - - - 1 Sofie Symoens
+?/+? 1 c.16C>T r.(?) p.(Arg6Trp) - - Unknown - pathogenic (recessive) g.1167674C>T g.1232294C>T - - B3GALT6_000007 - - - - Unknown yes - - - - - - - - - - - - - - - - - - - - - -
+/+? 1 c.16C>T r.(?) p.(Arg6Trp) missense substitution Parent #1 - likely pathogenic g.1167674C>T - - - B3GALT6_000007 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - EDS, EDSSPD1 P12 PubMed: Nakajima et al., 2013 - - - Brazil - - - - - 1 Raymond Dalgleish
+?/+? 1 c.16C>T r.(?) p.(Arg6Trp) missense substitution Unknown - likely pathogenic g.1167674C>T - - - B3GALT6_000007 - PubMed: Vorster et al., 2014 - - Unknown - - - - - DNA SEQ - - SEMDJL1 F1 PubMed: Vorster et al., 2014 The patient had an unaffected sibling who only carried the c.16C>T variant. - - South Africa Afrikaner - - - - 1 Raymond Dalgleish
-?/. - c.17G>A r.(?) p.(Arg6Gln) - - Unknown - likely benign g.1167675G>A - B3GALT6(NM_080605.4):c.17G>A (p.R6Q) - B3GALT6_000063 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.22_36dup r.(?) p.(Trp8_Ala12dup) - - Unknown - likely benign g.1167680_1167694dup - B3GALT6(NM_080605.4):c.22_36dupTGGCGGCGGCGGGCG (p.W8_A12dup) - B3GALT6_000059 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.77T>C r.(?) p.(Leu26Pro) missense substitution Unknown - pathogenic g.1167735T>C - - - B3GALT6_000020 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 The technique used was the custom NGS Gene panel. - - France French - - - - 1 Sofie Symoens
?/. - c.181G>C r.(?) p.(Val61Leu) - - Unknown - VUS g.1167839G>C g.1232459G>C - - B3GALT6_000022 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.181G>C r.(?) p.(Val61Leu) missense substitution Unknown - pathogenic g.1167839G>C - - - B3GALT6_000022 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 A non-consanguineous couple of Caucasian origin had two pregnancies terminated because of severe skeletal dysplasia. The second pregnancy was assigned the Patient ID AN_005849.The technique used was whole exome sequencing. - - Netherlands Dutch - - - - 1 Sofie Symoens
+?/. 1 c.182T>C r.(?) p.(Val61Ala) - - Paternal (confirmed) - likely pathogenic g.1167840T>C g.1232460T>C - - B3GALT6_000041 - - - - Germline yes - - - - DNA PCR Blood - SEMDJL1 - - - M no - - - - - - 1 Cynthia Silveira
+?/+? 1 c.193A>G r.(?) p.(Ser65Gly) missense substitution Parent #2 - likely pathogenic g.1167851A>G - - - B3GALT6_000032 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 P7 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would result in a 41aa deletion due to the second ATG becoming the initiating codon. The technique used was whole exome sequencing. - - Japan;Singapore Japanese/Singaporean - - - - 1 Raymond Dalgleish
+/+ 1 c.197_253del r.(?) p.(Ala66_Arg84del) deletion deletion Unknown - pathogenic g.1167855_1167911del - - - B3GALT6_000014 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 This patient (PIV:1) has two affected siblings with IDs AN_005842 and AN_005843. - - Congo;Rwanda Congolese-Rwandan - - - - 1 Sofie Symoens
+?/+? 1 c.200C>T r.(?) p.(Pro67Leu) missense substitution Parent #2 - likely pathogenic g.1167858C>T - - - B3GALT6_000033 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - SEMDJL1 P8 PubMed: Nakajima et al., 2013 - - - Viet Nam Vietnamese - - - - 1 Raymond Dalgleish
+?/+? 1 c.200C>T r.(?) p.(Pro67Leu) missense substitution Paternal (confirmed) - likely pathogenic g.1167858C>T - - - B3GALT6_000033 - PubMed: Honey et al., 2016 - - Unknown - - - - - DNA ? - - SEMDJL1 Family 1 PubMed: Honey et al., 2016 The patient had a brother who was also positive for both variants, and had a similar phenotype. - - South Africa Afrikaner - - - - 1 Raymond Dalgleish
+/+? 1 c.200C>T r.(?) p.(Pro67Leu) missense substitution Maternal (confirmed) - likely pathogenic g.1167858C>T - - - B3GALT6_000033 - PubMed: Honey et al., 2016 - - Unknown - - - - - DNA ? - - SEMDJL1 Family 2 PubMed: Honey et al., 2016 - - - - - - - - - 1 Raymond Dalgleish
+?/+? 1 c.200C>T r.(?) p.(Pro67Leu) missense substitution Unknown - likely pathogenic g.1167858C>T - - - B3GALT6_000033 - PubMed: Vorster et al., 2014 - - Unknown - - - - - DNA SEQ - - SEMDJL1 F1 PubMed: Vorster et al., 2014 The patient had an unaffected sibling who only carried the c.16C>T variant. - - South Africa Afrikaner - - - - 1 Raymond Dalgleish
+/+ 1 c.227del r.(?) p.(Ile76Thrfs*202) frameshift deletion Maternal (confirmed) - pathogenic g.1167885del - - - B3GALT6_000037 - PubMed: Ritelli et al., 2015 - - Unknown - - - - - DNA SEQ-NG, SEQ - - SEMDJL1 Patient 1 PubMed: Ritelli et al., 2015 The patient had a younger sister who carried both variants and had a similar phenotype. The technique used was the custom NGS Gene panel. - - - - - - - - 1 Raymond Dalgleish
+?/+? 1 c.235A>G r.(?) p.(Thr79Ala) missense substitution Maternal (inferred) - likely pathogenic g.1167893A>G - - - B3GALT6_000034 - PubMed: Honey et al., 2016 - - Unknown - - - - - DNA ? - - SEMDJL1 Family 1 PubMed: Honey et al., 2016 The patient had a brother who was also positive for both variants, and had a similar phenotype. - - South Africa Afrikaner - - - - 1 Raymond Dalgleish
+/+? 1 c.235A>G r.(?) p.(Thr79Ala) missense substitution Paternal (confirmed) - likely pathogenic g.1167893A>G - - - B3GALT6_000034 - PubMed: Honey et al., 2016 - - Unknown - - - - - DNA ? - - SEMDJL1 Family 2 PubMed: Honey et al., 2016 - - - - - - - - - 1 Raymond Dalgleish
+?/+? 1 c.235A>G r.(?) p.(Thr79Ala) missense substitution Both (homozygous) - likely pathogenic g.1167893A>G - - - B3GALT6_000034 - PubMed: Vorster et al., 2014 - - Unknown - - - - - DNA SEQ - - SEMDJL1 F3 PubMed: Vorster et al., 2014 - - - - - - - - - 1 Raymond Dalgleish
+?/+? 1 c.235A>G r.(?) p.(Thr79Ala) missense substitution Both (homozygous) - likely pathogenic g.1167893A>G - - - B3GALT6_000034 - PubMed: Vorster et al., 2014 - - Unknown - - - - - DNA SEQ - - SEMDJL1 F8 PubMed: Vorster et al., 2014 One unaffected parent's B3GALT6 gene was sequenced and shown to be heterozygous for c.235A>G. - - South Africa Afrikaner - - - - 1 Raymond Dalgleish
+?/+? 1 c.235A>G r.(?) p.(Thr79Ala) missense substitution Both (homozygous) - likely pathogenic g.1167893A>G - - - B3GALT6_000034 - PubMed: Vorster et al., 2014 - - Unknown - - - - - DNA SEQ - - SEMDJL1 F10 PubMed: Vorster et al., 2014 - - - South Africa Afrikaner - - - - 1 Raymond Dalgleish
-/- 1 c.308C>T r.(?) p.(Ala103Val) missense substitution Paternal (confirmed) - likely benign g.1167966C>T - - - B3GALT6_000026 - PubMed: Caraffi et al., 2019 - - Unknown - - - - - DNA SEQ-NG, PCR, SEQ - - EDS, EDSSPD1 Patient 3 PubMed: Caraffi et al., 2019 The patient was the second child of non-consanguineous parents. Three variants were detected, and variant c.308C>T was described as a variant of uncertain significance. The technique used was the custom NGS Gene panel. - - - - - - - - 1 Raymond Dalgleish
+/+ 1 c.323_344del r.(?) p.(Ala108Glyfs∗163) nonsense deletion Parent #1 - pathogenic g.1167981_1168002del - - - B3GALT6_000002 - PubMed: Malfait et al., 2013 - - Unknown - - - - - DNA RT-PCR, SEQ - - EDS, EDSSPD2 P3 PubMed: Malfait et al., 2013 Has a younger sister, P4, of the same genotype - - Iran - - - - - 1 Raymond Dalgleish
-?/. - c.324C>A r.(?) p.(Ala108=) - - Unknown - likely benign g.1167982C>A g.1232602C>A B3GALT6(NM_080605.4):c.324C>A (p.A108=) - B3GALT6_000053 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.353del r.(?) p.(Asp118Alafs*160) nonsense deletion Parent #1 - pathogenic g.1168011del - - - B3GALT6_000004 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - EDS, EDSSPD1 P9 PubMed: Nakajima et al., 2013 This patient was further described in {PMID31614862:Caraffi et al., 2019} - - Italy Italy - - - - 1 Raymond Dalgleish
+/+ 1 c.353del r.(?) p.(Asp118Alafs*160) nonsense deletion Paternal (confirmed) - pathogenic g.1168011del - - - B3GALT6_000004 - PubMed: Caraffi et al., 2019 - - Unknown - - - - - DNA SEQ-NG, PCR, SEQ - - EDS, EDSSPD1 Patient 3 PubMed: Caraffi et al., 2019 The patient was the second child of non-consanguineous parents. Three variants were detected, and variant c.308C>T was described as a variant of uncertain significance. The technique used was the custom NGS Gene panel. - - - - - - - - 1 Raymond Dalgleish
?/. - c.381C>G r.(?) p.(Asp127Glu) - - Unknown - VUS g.1168039C>G - B3GALT6(NM_080605.4):c.381C>G (p.D127E) - B3GALT6_000060 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+? 1 c.415_423del r.(?) p.(Met139Ala141del) deletion deletion Parent #2 - likely pathogenic g.1168073_1168081del - - - B3GALT6_000008 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - EDS, EDSSPD1 P12 PubMed: Nakajima et al., 2013 - - - Brazil - - - - - 1 Raymond Dalgleish
?/. - c.426G>T r.(?) p.(Trp142Cys) - - Unknown - VUS g.1168084G>T - - - B3GALT6_000067 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.430G>A r.(?) p.(Asp144Asn) - - Unknown - VUS g.1168088G>A g.1232708G>A - - B3GALT6_000018 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.430G>A r.(?) p.(Asp144Asn) missense substitution Unknown - pathogenic g.1168088G>A - - - B3GALT6_000018 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - Netherlands Dutch - - - - 1 Sofie Symoens
+?/+? 1 c.466G>A r.(?) p.(Asp156Asn) missense substitution Parent #2 - likely pathogenic g.1168124G>A - - - B3GALT6_000030 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 Patient 3 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would cause a 41 amino acid deletion due to the second ATG becoming the initiating codon. The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+/+ 1 c.476C>A r.(?) p.(Ser159Tyr) missense substitution Maternal (confirmed) - pathogenic g.1168134C>A - - - B3GALT6_000024 - PubMed: Sellars et al., 2014 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Sellars et al., 2014 The authors have confirmed the transcript-level sequence variants that cause the amino acid substitutions.The technique used was whole exome sequencing. - - - - - - - - 1 Raymond Dalgleish
-?/. - c.477C>T r.(?) p.(Ser159=) - - Unknown - likely benign g.1168135C>T - B3GALT6(NM_080605.4):c.477C>T (p.S159=) - B3GALT6_000064 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.477del r.(?) p.(Phe160Serfs*118) frameshift deletion Unknown - pathogenic g.1168135del - - - B3GALT6_000012 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - Netherlands Dutch - - - - 1 Sofie Symoens
-?/. - c.483G>A r.(?) p.(Ala161=) - - Unknown - likely benign g.1168141G>A - B3GALT6(NM_080605.4):c.483G>A (p.A161=) - B3GALT6_000061 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.483G>A r.(?) p.(Ala161=) - - Unknown - likely benign g.1168141G>A - B3GALT6(NM_080605.4):c.483G>A (p.A161=) - B3GALT6_000061 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/+ - c.510_517del r.(?) p.(Glu174Alafs*266) frameshift deletion Paternal (inferred) ACMG likely pathogenic g.1168168_1168175del g.1232791_1232798del - - B3GALT6_000065 - PubMed: Shen et al., 2022 - - Germline - - - - - DNA SEQ-NG-I peripheral blood - EDSSPD I-1 PubMed: Shen et al., 2022 - M no China - - - - - 1 Oumaima Nehaili
+?/. - c.510_517del r.(?) p.(Glu174Alafs*266) deletion deletion Paternal (confirmed) ACMG likely pathogenic g.1168168_1168175del g.1232791_1232798del - - B3GALT6_000065 - PubMed: Shen et al., 2022 - - Germline - - - - - DNA SEQ-NG-I Peripheral blood - EDSSPD III-2 PubMed: Shen et al., 2022 - M no China - - - - - 1 Oumaima Nehaili
+?/+? 1 c.511C>T r.(?) p.(Arg171Cys) missense substitution Paternal (confirmed) - likely pathogenic g.1168169C>T - - - B3GALT6_000036 - PubMed: Trejo et al., 2017 - - Unknown - - - - - DNA SEQ - - SEMDJL1 IV-5 PubMed: Trejo et al., 2017 The proband also had two siblings who carried both variants in B3GALT6, and were positive for SEMDJL, with some clinical variability. They were also described in {PMID28229453:Ranza et al., 2017} - - - - - - - - 1 Raymond Dalgleish
+/+ 1 c.513_520del r.(?) p.(Glu174Alafs*266) frameshift deletion Unknown - pathogenic g.1168171_1168178del - - - B3GALT6_000011 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 The technique used was the custom NGS Gene panel. - - United States USA - - - - 1 Sofie Symoens
+/+ 1 c.513_520del r.(?) p.(Glu174Alafs*266) frameshift deletion Unknown - pathogenic g.1168171_1168178del - - - B3GALT6_000011 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - Netherlands Dutch - - - - 1 Sofie Symoens
+/+ 1 c.513_520del r.(?) p.(Glu174Alafs*266) frameshift deletion Unknown - pathogenic g.1168171_1168178del - - - B3GALT6_000011 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 A non-consanguineous couple of Caucasian origin had two pregnancies terminated because of severe skeletal dysplasia. The second pregnancy was assigned the Patient ID AN_005849.The technique used was whole exome sequencing. - - Netherlands Dutch - - - - 1 Sofie Symoens
-?/. - c.515C>T r.(?) p.(Ala172Val) - - Unknown - likely benign g.1168173C>T g.1232793C>T B3GALT6(NM_080605.4):c.515C>T (p.A172V) - B3GALT6_000043 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.515C>T r.(?) p.(Ala172Val) - - Unknown - likely benign g.1168173C>T g.1232793C>T B3GALT6(NM_080605.4):c.515C>T (p.A172V) - B3GALT6_000043 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.519C>T r.(?) p.(Arg173=) - - Unknown - likely benign g.1168177C>T g.1232797C>T B3GALT6(NM_080605.4):c.519C>T (p.R173=) - B3GALT6_000054 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.522G>C r.(?) p.(Glu174Asp) - - Unknown - benign g.1168180G>C g.1232800G>C B3GALT6(NM_080605.4):c.522G>C (p.E174D) - B3GALT6_000044 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.536_541dup r.(?) p.(Arg179_Arg180dup) duplication duplication Both (homozygous) - pathogenic g.1168194_1168199dup - - - B3GALT6_000025 - PubMed: Alazami et al., 2016 - - Unknown - - - - - DNA SEQ, SEQ-NG - - EDS, EDSSPD2 Family 9 PubMed: Alazami et al., 2016 The formal ID for this family is 12DG2007.The technique used was whole exome sequencing. - - - - - - - - 1 Raymond Dalgleish
+/. - c.536_541dup r.(?) p.(Arg179_Arg180dup) - - Both (homozygous) - pathogenic (recessive) g.1168194_1168199dup g.1232814_1232819dup NM_080605.3:c.536_541dupGCCGCC:p.(Arg179_Arg180dup) - B3GALT6_000025 - PubMed: Maddirevula 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES skeletal dysplasia 12DG2007 PubMed: Maddirevula 2018 isolated case F yes - Arab - - - - 1 LOVD
-?/. - c.540C>A r.(?) p.(Arg180=) - - Unknown - likely benign g.1168198C>A g.1232818C>A B3GALT6(NM_080605.4):c.540C>A (p.R180=) - B3GALT6_000055 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.545A>G r.(?) p.(Tyr182Cys) missense substitution Both (homozygous) - pathogenic g.1168203A>G - - - B3GALT6_000019 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - Iran Iranian - - - - 1 Sofie Symoens
+/+ 1 c.556T>C r.(?) p.(Phe186Leu) missense substitution Both (homozygous) - pathogenic g.1168214T>C - - - B3GALT6_000023 - PubMed: Alazami et al., 2016 - - Unknown - - - - - DNA SEQ, SEQ-NG - - EDS, EDSSPD2 Family 6 PubMed: Alazami et al., 2016 The proband has an affected cousin.The formal ID for this family is 12DG0715.The technique used was whole exome sequencing. - - - - - - - - 1 Raymond Dalgleish
+/+ 1 c.556T>C r.(?) p.(Phe186Leu) missense substitution Both (homozygous) - pathogenic g.1168214T>C - - - B3GALT6_000023 - PubMed: Alazami et al., 2016 - - Unknown - - - - - DNA SEQ, SEQ-NG - - EDS, EDSSPD2 Family 7 PubMed: Alazami et al., 2016 There are two affected individuals in this family.The formal ID for this family is 12DG1291.The technique used was whole genome sequencing. - - - - - - - - 1 Raymond Dalgleish
+/+ 1 c.556T>C r.(?) p.(Phe186Leu) missense substitution Both (homozygous) - pathogenic g.1168214T>C - - - B3GALT6_000023 - PubMed: Alazami et al., 2016 - - Unknown - - - - - DNA SEQ, SEQ-NG - - EDS, EDSSPD2 Family 8 PubMed: Alazami et al., 2016 The formal ID for this family is 12DG2397.The technique used was whole genome sequencing. - - - - - - - - 1 Raymond Dalgleish
+/. - c.556T>C r.(?) p.(Phe186Leu) - - Both (homozygous) - pathogenic (recessive) g.1168214T>C g.1232834T>C NM_080605.3:c.556T>C:p.(Phe186Leu) - B3GALT6_000023 - PubMed: Maddirevula 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES skeletal dysplasia 12DG0715 PubMed: Maddirevula 2018 isolated case F yes - Arab - - - - 1 LOVD
+/. - c.556T>C r.(?) p.(Phe186Leu) - - Both (homozygous) - pathogenic (recessive) g.1168214T>C g.1232834T>C NM_080605.3:c.556T>C:p.(Phe186Leu) - B3GALT6_000023 - PubMed: Maddirevula 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES skeletal dysplasia 12DG1291, 12DG1024 PubMed: Maddirevula 2018 family, 2 affected (F, M) F;M yes - Arab - - - - 2 LOVD
+/. - c.556T>C r.(?) p.(Phe186Leu) - - Both (homozygous) - pathogenic (recessive) g.1168214T>C g.1232834T>C NM_080605.3:c.556T>C:p.(Phe186Leu) - B3GALT6_000023 - PubMed: Maddirevula 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES skeletal dysplasia 12DG2397 PubMed: Maddirevula 2018 family F yes - Arab - - - - 1 LOVD
+/. - c.556T>C r.(?) p.(Phe186Leu) - - Both (homozygous) - pathogenic (recessive) g.1168214T>C g.1232834T>C NM_080605.3:c.556T>C:p.(Phe186Leu) - B3GALT6_000023 - PubMed: Maddirevula 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES skeletal dysplasia 12DG1024 PubMed: Maddirevula 2018 family F yes - Arab - - - - 1 LOVD
+/+ 1 c.588del r.(?) p.(Arg197Alafs∗81) nonsense deletion Parent #1 - pathogenic g.1168246del - - - B3GALT6_000006 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - EDS, EDSSPD1 P10 PubMed: Nakajima et al., 2013 P10, of family F9, has a younger female relative of the same genotype (relation not explicitly stated, probably a sister) - - Italy;Canada Italian/Canadian - - - - 1 Raymond Dalgleish
+/. 1 c.588dup r.(?) p.(Arg197Alafs*246) - - Unknown - pathogenic g.1168246dup g.1232866dup 588dup - B3GALT6_000042 - - - - Germline - - - - - DNA PCR Blood - SEMDJL1 - - - M no - - - - - - 1 Cynthia Silveira
+?/. - c.588dup r.(?) p.(Arg197AlafsTer246) - - Unknown - likely pathogenic g.1168246dup - B3GALT6(NM_080605.3):c.588dup (p.(Arg197Alafs*246)), B3GALT6(NM_080605.4):c.588dupG (p.R197Afs*246) - B3GALT6_000042 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/. - c.588dup r.(?) p.(Arg197AlafsTer246) - - Unknown - likely pathogenic g.1168246dup - B3GALT6(NM_080605.3):c.588dup (p.(Arg197Alafs*246)), B3GALT6(NM_080605.4):c.588dupG (p.R197Afs*246) - B3GALT6_000042 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+? 1 c.618C>G r.(?) p.(Cys206Trp) missense substitution Both (homozygous) - likely pathogenic g.1168276C>G - - - B3GALT6_000039 - PubMed: Ben-Mahmoud et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - ALGAZ V-2 PubMed: Ben-Mahmoud et al., 2018 This family was previously described in PubMed: Al-Gazali et al., 1999. The proband had two siblings V-1, and V-2, who carried the same variants and phenotype. The authors of {PMID29443383:Ben-Mahmoud et al., 2018} suggest that Al-Gazali syndrome represents the more severe phenotype among B3GALT6-related diseases due to patients dying within the first few months of life. - - Palestine Palestinian - - - - 1 Raymond Dalgleish
+/+ 1 c.619G>C r.(?) p.(Asp207His) missense substitution Both (homozygous) - pathogenic g.1168277G>C - - - B3GALT6_000001 - PubMed: Malfait et al., 2013 - - Unknown - - - - - DNA PCR, SEQ, arraySEQ - - EDS, EDSSPD2 P1 PubMed: Malfait et al., 2013 P1 has a maternal cousin, P2, of the same genotype - - Iran - - - - - 1 Raymond Dalgleish
+/+ 1 c.619G>C r.(?) p.(Asp207His) missense substitution Parent #2 - pathogenic g.1168277G>C - - - B3GALT6_000001 - PubMed: Malfait et al., 2013 - - Unknown - - - - - DNA RT-PCR, SEQ - - EDS, EDSSPD2 P3 PubMed: Malfait et al., 2013 Has a younger sister, P4, of the same genotype - - Iran - - - - - 1 Raymond Dalgleish
-?/. - c.630G>A r.(?) p.(Leu210=) - - Unknown - likely benign g.1168288G>A g.1232908G>A B3GALT6(NM_080605.4):c.630G>A (p.L210=) - B3GALT6_000045 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.631C>T r.(?) p.(Pro211Ser) missense substitution Unknown - pathogenic g.1168289C>T - - - B3GALT6_000017 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - India Indian - - - - 1 Sofie Symoens
+/+ 1 c.649G>A r.(?) p.(Gly217Ser) missense substitution Both (homozygous) - pathogenic g.1168307G>A - - - B3GALT6_000003 - PubMed: Malfait et al., 2013 - - Unknown - - - - - DNA RT-PCR, SEQ - - EDS, EDSSPD2 P5 PubMed: Malfait et al., 2013 - - - Iran - - - - - 1 Raymond Dalgleish
+?/+? 1 c.694C>T r.(?) p.(Arg232Cys) missense substitution Parent #2 - likely pathogenic g.1168352C>T - - - B3GALT6_000029 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 P5 PubMed: Nakajima et al., 2013 The authors predicted the c.1A>G variant would result in a 41 aa deletion due to the second ATG becoming the initiating codon. The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.694C>T r.(?) p.(Arg232Cys) missense substitution Parent #2 - likely pathogenic g.1168352C>T - - - B3GALT6_000029 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 Patient 1 PubMed: Nakajima et al., 2013 The patient had a sibling who was also compound heterozygous for both variants and had a similar phenotype.c.1A>G showed a decreased molecular weight ~4kD lower compared to the WT protein. The authors suggested that the translation initiation at the second ATG of the coding sequence (position c.124) would become the initiation codon, resulting in a protein change of p.Met1_Ala41del.The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.694C>T r.(?) p.(Arg232Cys) missense substitution Parent #1 - likely pathogenic g.1168352C>T - - - B3GALT6_000029 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 P6 PubMed: Nakajima et al., 2013 The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.694C>T r.(?) p.(Arg232Cys) missense substitution Parent #1 - likely pathogenic g.1168352C>T - - - B3GALT6_000029 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - SEMDJL1 P8 PubMed: Nakajima et al., 2013 - - - Viet Nam Vietnamese - - - - 1 Raymond Dalgleish
-?/. - c.735G>C r.(?) p.(Leu245=) - - Unknown - likely benign g.1168393G>C g.1233013G>C B3GALT6(NM_080605.4):c.735G>C (p.L245=) - B3GALT6_000056 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/+? 1 c.766C>T r.(?) p.(Arg256Trp) missense substitution Paternal (confirmed) - likely pathogenic g.1168424C>T - - - B3GALT6_000038 - PubMed: Ritelli et al., 2015 - - Unknown - - - - - DNA SEQ-NG, SEQ - - SEMDJL1 Patient 1 PubMed: Ritelli et al., 2015 The patient had a younger sister who carried both variants and had a similar phenotype. The technique used was the custom NGS Gene panel. - - - - - - - - 1 Raymond Dalgleish
+/+ 1 c.782G>A r.(?) p.(Arg261His) missense substitution Unknown - pathogenic g.1168440G>A - - - B3GALT6_000013 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 - - - Netherlands Dutch - - - - 1 Sofie Symoens
+/+ 1 c.795A>C r.(?) p.(Glu265Asp) missense substitution Unknown - pathogenic g.1168453A>C - - - B3GALT6_000009 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 The technique used was whole exome sequencing. - - United States USA - - - - 1 Sofie Symoens
+/+ 1 c.795A>C r.(?) p.(Glu265Asp) missense substitution Paternal (confirmed) - pathogenic g.1168453A>C - - - B3GALT6_000009 - PubMed: Sellars et al., 2014 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Sellars et al., 2014 The authors have confirmed the transcript-level sequence variants that cause the amino acid substitutions.The technique used was whole exome sequencing. - - - - - - - - 1 Raymond Dalgleish
+/+ 1 c.808G>A r.(?) p.(Gly270Ser) missense substitution Unknown - pathogenic g.1168466G>A - - - B3GALT6_000021 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 The technique used was the custom NGS Gene panel. - - France French - - - - 1 Sofie Symoens
?/. - c.818A>G r.(?) p.(Asn273Ser) - - Unknown - VUS g.1168476A>G - B3GALT6(NM_080605.3):c.818A>G (p.(Asn273Ser)) - B3GALT6_000069 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.825C>T r.(?) p.(Tyr275=) - - Unknown - likely benign g.1168483C>T - B3GALT6(NM_080605.4):c.825C>T (p.Y275=) - B3GALT6_000062 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.833C>T r.(?) p.(Thr278Met) - - Unknown - VUS g.1168491C>T g.1233111C>T B3GALT6(NM_080605.4):c.833C>T (p.T278M) - B3GALT6_000057 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/+? 1 c.845_846delinsTA r.(?) p.(Ser282Ile) missense delins Both (homozygous) - likely pathogenic g.1168503_1168504delinsTA - - - B3GALT6_000040 - PubMed: Ranza et al., 2017 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 Patient 7 PubMed: Ranza et al., 2017 The patient initially had no clinical diagnosis, but was classified as having SEMDJL1 after molecular screening. The technique used was whole exome sequencing. - - - - - - - - 1 Raymond Dalgleish
+?/+? - c.883C>T r.(?) p.(Arg295Cys) missense substitution Unknown ACMG unclassified g.1168541C>T g.1233161C>T - - B3GALT6_000066 - PubMed: Shen et al., 2022 - - Germline - - - - - DNA SEQ-NG-I - - - - - - - - - - - - - - - -
+?/. - c.883C>T r.(?) p.(Arg295Cys) missense substitution Maternal (confirmed) ACMG unclassified g.1168541C>T g.1233161C>T - - B3GALT6_000066 - PubMed: Shen et al., 2022 - - Germline - - - - - DNA SEQ-NG-I Peripheral blood - EDSSPD III-2 PubMed: Shen et al., 2022 - M no China - - - - - 1 Oumaima Nehaili
?/. - c.895C>A r.(?) p.(Leu299Met) - - Unknown - VUS g.1168553C>A g.1233173C>A B3GALT6(NM_080605.4):c.895C>A (p.L299M) - B3GALT6_000058 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/+? 1 c.899G>C r.(?) p.(Cys300Ser) missense substitution Parent #2 - likely pathogenic g.1168557G>C - - - B3GALT6_000031 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ, SEQ-NG - - SEMDJL1 P6 PubMed: Nakajima et al., 2013 The technique used was whole exome sequencing. - - Japan Japanese - - - - 1 Raymond Dalgleish
+?/+? 1 c.901_921dup r.(?) p.(Lys301_Arg307dup) duplication duplication Maternal (confirmed) - likely pathogenic g.1168559_1168579dup - - - B3GALT6_000035 - PubMed: Trejo et al., 2017 - - Unknown - - - - - DNA SEQ - - SEMDJL1 IV-5 PubMed: Trejo et al., 2017 The proband also had two siblings who carried both variants in B3GALT6, and were positive for SEMDJL, with some clinical variability. They were also described in {PMID28229453:Ranza et al., 2017} - - - - - - - - 1 Raymond Dalgleish
+/+? 1 c.925T>A r.(?) p.(Ser309Thr) missense substitution Parent #2 - likely pathogenic g.1168583T>A - - - B3GALT6_000005 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - EDS, EDSSPD1 P9 PubMed: Nakajima et al., 2013 This patient was further described in {PMID31614862:Caraffi et al., 2019} - - Italy Italy - - - - 1 Raymond Dalgleish
+/+? 1 c.925T>A r.(?) p.(Ser309Thr) missense substitution Parent #2 - likely pathogenic g.1168583T>A - - - B3GALT6_000005 - PubMed: Nakajima et al., 2013 - - Unknown - - - - - DNA SEQ - - EDS, EDSSPD1 P10 PubMed: Nakajima et al., 2013 P10, of family F9, has a younger female relative of the same genotype (relation not explicitly stated, probably a sister) - - Italy;Canada Italian/Canadian - - - - 1 Raymond Dalgleish
+/+ 1 c.925T>A r.(?) p.(Ser309Thr) missense substitution Unknown - pathogenic g.1168583T>A - - - B3GALT6_000005 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 The technique used was the custom NGS Gene panel. - - United States USA - - - - 1 Sofie Symoens
+/+ 1 c.929A>G r.(?) p.(Tyr310Cys) missense substitution Unknown - pathogenic g.1168587A>G - - - B3GALT6_000010 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA SEQ-NG - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 The technique used was whole exome sequencing. - - United States USA - - - - 1 Sofie Symoens
-?/. - c.930C>T r.(?) p.(Tyr310=) - - Unknown - likely benign g.1168588C>T - B3GALT6(NM_080605.4):c.930C>T (p.Y310=) - B3GALT6_000068 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 1 c.953C>T r.(?) p.(Pro318Leu) missense substitution Unknown - pathogenic g.1168611C>T - - - B3GALT6_000015 - PubMed: Van Damme et al., 2018 - - Unknown - - - - - DNA PCR, SEQ - - EDS, EDSSPD2 - PubMed: Van Damme et al., 2018 This patient (PIV:1) has two affected siblings with IDs AN_005842 and AN_005843. - - Congo;Rwanda Congolese-Rwandan - - - - 1 Sofie Symoens
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