Full data view for gene SPTLC2

This database is one of the gene variant databases from the Leiden Muscular Dystrophy pages
Information The variants shown are described using the NM_004863.3 transcript reference sequence.

55 entries on 1 page. Showing entries 1 - 55.
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Effect     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

Allele     

Classification method     

Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

Published as     

ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

Origin     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Template     

Technique     

Tissue     

Remarks     

Disease     

ID_report     

Reference     

Remarks     

Gender     

Consanguinity     

Country     

Population     

Age at death     

VIP     

Data_av     

Treatment     

Panel size     

Owner     
-?/. - c.81C>T r.(?) p.(Asn27=) Unknown - likely benign g.78082842G>A g.77616499G>A SPTLC2(NM_004863.3):c.81C>T (p.N27=) - SPTLC2_000037 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.117_122dup r.(?) p.(Ala41_Ala42dup) Unknown - VUS g.78082815_78082820dup - SPTLC2(NM_004863.3):c.122_123insAGCCGC (p.(Ala40_Ala41dup)) - SPTLC2_000045 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.162A>C r.(?) p.(Leu54=) Unknown - benign g.78063694T>G g.77597351T>G SPTLC2(NM_004863.3):c.162A>C (p.L54=) - SPTLC2_000035 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.300C>T r.(?) p.(His100=) Unknown - likely benign g.78063556G>A g.77597213G>A SPTLC2(NM_004863.3):c.300C>T (p.H100=) - SPTLC2_000038 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.327+89T>G r.(=) p.(=) Parent #1 - benign g.78063440A>C g.77597097A>C - - SPTLC2_000016 - - - rs12435993 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.328-17T>C r.(=) p.(=) Unknown - benign g.78045469A>G g.77579126A>G SPTLC2(NM_004863.3):c.328-17T>C - SPTLC2_000030 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/. - c.529A>C r.(?) p.(Asn177His) Unknown - likely pathogenic (dominant) g.78043212T>G g.77576869T>G - - SPTLC2_000044 - PubMed: Antoniadi 2015 - - Germline - - - 0 - DNA SEQ - 56-gene neuropathy panel HSN - PubMed: Antoniadi 2015 analysis 448 inherited peripheral neuropathy cases - - United Kingdom (Great Britain) - - 0 - - 1 Johan den Dunnen
+/. - c.544G>C r.(?) p.(Ala182Pro) Unknown - pathogenic (dominant) g.78043197C>G g.77576854C>G - - SPTLC2_000043 - PubMed: Antoniadi 2015 - - Germline - - - 0 - DNA SEQ - 56-gene neuropathy panel CMT-2 - PubMed: Antoniadi 2015 analysis 448 inherited peripheral neuropathy cases - - United Kingdom (Great Britain) - - 0 - - 1 Johan den Dunnen
?/. - c.547C>T r.(?) p.(Arg183Trp) Parent #1 - VUS g.78043194G>A g.77576851G>A - - SPTLC2_000015 PolyPhen-2: possibly damaging (PSIC: 0,764) - - - Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
?/. - c.631+130del r.(=) p.(=) Parent #1 - VUS g.78042980del g.77576637del - - SPTLC2_000014 - - - - Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.632-84T>C r.(=) p.(=) Parent #1 - benign g.78036935A>G g.77570592A>G - - SPTLC2_000021 - - - rs4903603 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.632-49del r.(=) p.(=) Parent #1 - benign g.78036900del g.77570557del - - SPTLC2_000020 - - - rs11344772 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-?/. - c.723G>A r.(?) p.(Thr241=) Unknown - likely benign g.78036760C>T g.77570417C>T SPTLC2(NM_004863.3):c.723G>A (p.T241=) - SPTLC2_000029 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.723G>T r.(?) p.(Thr241=) Unknown - benign g.78036760C>A g.77570417C>A SPTLC2(NM_004863.3):c.723G>T (p.T241=) - SPTLC2_000034 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.756+69G>C r.(=) p.(=) Parent #1 - benign g.78036658C>G g.77570315C>G - - SPTLC2_000019 - - - rs76545605 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
?/. - c.761G>C r.(?) p.(Cys254Ser) Unknown - VUS g.78028828C>G g.77562485C>G SPTLC2(NM_004863.3):c.761G>C (p.C254S) - SPTLC2_000039 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.786T>C r.(=) p.(=) Parent #1 - benign g.78028803A>G g.77562460A>G - - SPTLC2_000010 - - - rs2364602 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.786T>C r.(?) p.(Asn262=) Unknown - benign g.78028803A>G g.77562460A>G SPTLC2(NM_004863.3):c.786T>C (p.N262=) - SPTLC2_000010 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.786T>C r.(?) p.(Asn262=) Unknown - benign g.78028803A>G g.77562460A>G SPTLC2(NM_004863.3):c.786T>C (p.N262=) - SPTLC2_000010 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.821G>C r.(?) p.(Gly274Ala) Unknown - VUS g.78028768C>G g.77562425C>G SPTLC2(NM_004863.3):c.821G>C (p.(Gly274Ala)) - SPTLC2_000033 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.850+34G>A r.(=) p.(=) Parent #1 - benign g.78028705C>T g.77562362C>T - - SPTLC2_000009 - - - rs45613436 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.851-30G>C r.(=) p.(=) Parent #1 - benign g.78023519C>G g.77557176C>G - - SPTLC2_000008 - - - - Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-?/. - c.853A>G r.(?) p.(Met285Val) Unknown - likely benign g.78023487T>C g.77557144T>C - - SPTLC2_000022 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/. - c.893A>G r.(?) p.(Tyr298Cys) Unknown - likely pathogenic (dominant) g.78023447T>C g.77557104T>C - - SPTLC2_000042 - PubMed: Antoniadi 2015 - - Germline - - - 0 - DNA SEQ - 56-gene neuropathy panel HMN - PubMed: Antoniadi 2015 analysis 448 inherited peripheral neuropathy cases - - United Kingdom (Great Britain) - - 0 - - 1 Johan den Dunnen
?/. - c.957-22A>G r.(=) p.(=) Parent #1 - VUS g.78021884T>C g.77555541T>C - - SPTLC2_000007 - - - - Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
?/. - c.977G>A r.(?) p.(Arg326His) Unknown - VUS g.78021842C>T g.77555499C>T SPTLC2(NM_004863.3):c.977G>A (p.R326H) - SPTLC2_000032 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1050C>T r.(?) p.(Gly350=) Unknown - likely benign g.78021769G>A g.77555426G>A SPTLC2(NM_004863.3):c.1050C>T (p.G350=) - SPTLC2_000028 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.1065A>T r.(?) p.(Thr355=) Unknown - benign g.78021754T>A g.77555411T>A SPTLC2(NM_004863.3):c.1065A>T (p.T355=) - SPTLC2_000027 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/. - c.1075G>A r.(?) p.(Val359Met) Unknown - pathogenic g.78021744C>T g.77555401C>T SPTLC2(NM_004863.3):c.1075G>A (p.V359M) - SPTLC2_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/. 11 c.1075G>A r.(?) p.(Val359Met) Unknown - pathogenic g.78021744C>T g.77555401C>T - - SPTLC2_000001 - PubMed: Rotthier 2010 - - Germline - - - 0 - DNA SEQ - - HSAN 20920666-FamCMT747PatI1 PubMed: Rotthier 2010 2-generation family, 1 affected F - Austria - - 0 - - 1 Johan den Dunnen
+?/. - c.1142T>C r.(?) p.(Phe381Ser) Unknown - likely pathogenic (dominant) g.78021677A>G g.77555334A>G - - SPTLC2_000041 - PubMed: Antoniadi 2015 - - Germline - - - 0 - DNA SEQ - 56-gene neuropathy panel HSN Pat17 PubMed: Antoniadi 2015 analysis 448 inherited peripheral neuropathy cases - - United Kingdom (Great Britain) - - 0 - - 1 Johan den Dunnen
+/. - c.1145G>T r.(?) p.(Gly382Val) Unknown - pathogenic g.78021674C>A g.77555331C>A SPTLC2(NM_004863.3):c.1145G>T (p.G382V) - SPTLC2_000002 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/. 13 c.1145G>T r.(?) p.(Gly382Val) Unknown - pathogenic g.78021674C>A g.77555331C>A - - SPTLC2_000002 - PubMed: Rotthier 2010 - - Germline - - - 0 - DNA SEQ - - HSAN 20920666-FamCMT117 PubMed: Rotthier 2010 2-generation family, 1 affected mother/son F;M no Austria - - 0 - - 2 Johan den Dunnen
+/. 13 c.1145G>T r.(?) p.(Gly382Val) Unknown - pathogenic g.78021674C>A g.77555331C>A - - SPTLC2_000002 - PubMed: Rotthier 2010 - - Germline/De novo (untested) - - - 0 - DNA SEQ - - HSAN 20920666-FamCMT1044 PubMed: Rotthier 2010 2-generation family, 1 affected, unaffected non-carrier relatives F - Germany - - 0 - - 1 Johan den Dunnen
+?/. - c.1148C>T r.(?) p.(Ala383Val) Parent #1 ACMG likely pathogenic g.78021671G>A g.77555328G>A - - SPTLC2_000031 ACMG ps3, pm1, pm2 PubMed: Dohrn 2017, Journal: Dohrn 2017 - - Germline - 1/612 cases - 0 - DNA SEQ, SEQ-NG - targeted multigene panel HSAN 28902413-Pat56 PubMed: Dohrn 2017, Journal: Dohrn 2017 analysis 612 patients M - (Germany) - - 0 - - 1 Johan den Dunnen
+/. - c.1151C>T r.(?) p.(Ser384Phe) Unknown - pathogenic g.78021668G>A g.77555325G>A SPTLC2(NM_004863.3):c.1151C>T (p.S384F) - SPTLC2_000026 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.1176+7G>A r.(=) p.(=) Unknown - likely benign g.78021636C>T g.77555293C>T SPTLC2(NM_004863.3):c.1176+7G>A - SPTLC2_000025 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.1176+98C>T r.(=) p.(=) Parent #1 - VUS g.78021545G>A g.77555202G>A - - SPTLC2_000006 - - - rs117989420 Germline - - - 0 - DNA SEQ - - ? - - - - - Germany - - 0 - - 1 Andreas Laner
?/. - c.1176+101A>G r.(=) p.(=) Parent #1 - VUS g.78021542T>C g.77555199T>C - - SPTLC2_000005 - - - - Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.1177-49G>A r.(=) p.(=) Parent #1 - benign g.78018614C>T g.77552271C>T - - SPTLC2_000004 - - - rs2178876 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-?/. - c.1227G>A r.(?) p.(Thr409=) Unknown - likely benign g.78018515C>T g.77552172C>T SPTLC2(NM_004863.3):c.1227G>A (p.T409=) - SPTLC2_000024 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.1304-14299C>T r.(=) p.(=) Unknown - benign g.78002223G>A g.77535880G>A SPTLC2(NM_004863.3):c.1304-14299C>T - SPTLC2_000023 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.1304-34G>T r.(=) p.(=) Parent #1 - benign g.77987958C>A g.77521615C>A - - SPTLC2_000013 - - - rs2072672 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.1304-34G>T r.(=) p.(=) Unknown - benign g.77987958C>A g.77521615C>A SPTLC2(NM_004863.3):c.1304-34G>T - SPTLC2_000013 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.1440-63G>A r.(=) p.(=) Parent #1 - benign g.77984573C>T g.77518230C>T - - SPTLC2_000012 - - - rs926114 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.1440-30T>G r.(=) p.(=) Parent #1 - benign g.77984540A>C g.77518197A>C - - SPTLC2_000011 - - - rs140089337 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
+/. - c.1510A>T r.(?) p.(Ile504Phe) Unknown - pathogenic g.77984440T>A g.77518097T>A SPTLC2(NM_004863.3):c.1510A>T (p.I504F) - SPTLC2_000003 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/. 15 c.1510A>T r.(?) p.(Ile504Phe) Unknown - pathogenic g.77984440T>A g.77518097T>A - - SPTLC2_000003 - PubMed: Rotthier 2010 - - De novo - - - 0 - DNA SEQ - - HSAN 20920666-FamCMT635 PubMed: Rotthier 2010 2-generation family, 1 affected, unaffected non-carrier parents M no Czech Republic - - 0 - - 1 Johan den Dunnen
+?/. - c.1513G>A r.(?) p.(Glu505Lys) Unknown - likely pathogenic (dominant) g.77984437C>T g.77518094C>T - - SPTLC2_000040 - PubMed: Antoniadi 2015 - - Germline - - - 0 - DNA SEQ - 56-gene neuropathy panel CMT-2 - PubMed: Antoniadi 2015 analysis 448 inherited peripheral neuropathy cases - - United Kingdom (Great Britain) - - 0 - - 1 Johan den Dunnen
?/. - c.1664C>T r.(?) p.(Thr555Met) Parent #1 - VUS g.77978652G>A g.77512309G>A - - SPTLC2_000017 - - - - Germline - - - 0 - DNA SEQ - - ? - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.1664C>T r.(?) p.(Thr555Met) Unknown - benign g.77978652G>A g.77512309G>A SPTLC2(NM_004863.3):c.1664C>T (p.T555M) - SPTLC2_000017 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.1664C>T r.(?) p.(Thr555Met) Unknown - likely benign g.77978652G>A g.77512309G>A SPTLC2(NM_004863.3):c.1664C>T (p.T555M) - SPTLC2_000017 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.1664C>T r.(?) p.(Thr555Met) Parent #1 - likely benign g.77978652G>A g.77512309G>A - - SPTLC2_000017 6 heterozygous, no homozygous; Clinindb (India) PubMed: Narang 2020, Journal: Narang 2020 - rs138652708 Germline - 6/2792 individuals - 0 - DNA arraySNP - Infinium Global Screening Array v1.0 ? - PubMed: Narang 2020, Journal: Narang 2020 analysis 2794 individuals (India) - - India - - 0 - - 6 Mohammed Faruq
-/. - c.*6T>G r.(=) p.(=) Parent #1 - benign g.77978621A>C g.77512278A>C - - SPTLC2_000018 - - - rs73319080 Germline - - - 0 - DNA SEQ - - - - - - - - Germany - - 0 - - 1 Andreas Laner
-/. - c.*6T>G r.(=) p.(=) Unknown - benign g.77978621A>C g.77512278A>C SPTLC2(NM_004863.3):c.*6T>G - SPTLC2_000018 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
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