Unique variants in the HMGCL gene

Information The variants shown are described using the NM_000191.2 transcript reference sequence.

77 entries on 1 page. Showing entries 1 - 77.
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Effect     

Reported     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

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     

Owner     
+/. 1 - c.? r.61_144del p.Val21_Lys48del - pathogenic (recessive) g.? - r.61-144del - NPHS2_000000 - PubMed: Alfadhel 2022, Journal: Alfadhel 2022 - - Germline - - - - - Johan den Dunnen
+/. 2 - c.27del r.(?) p.(Arg10Glyfs*24), p.(Arg10GlyfsTer24) - pathogenic (recessive) g.24151879del g.23825389del 27delG, c.27_27delG - HMGCL_000033 - PubMed: Grunert 2017, PubMed: Pospisilova 2003 - - Germline - - - - - Johan den Dunnen
+/. 5 1 c.31C>T r.(?) p.(Arg11*), p.(Arg11Ter) ACMG pathogenic (recessive) g.24151875G>A g.23825385G>A - - HMGCL_000050 Grünert 2017:28583327, Aoyama 2015:25872961, Puisac 2013:23465862 PubMed: Aoyama 2015, PubMed: Grunert 2017 ClinVar-521752 rs1212444447 Germline yes - - - - Johan den Dunnen, Miriam Erandi Reyna-Fabián
+/. 1 1i_4i c.61-540_348+22del r.? p.? - pathogenic (recessive) g.24143146_24147626del g.23816656_23821136del NG_013061 g.9326-13806del - HMGCL_000051 - PubMed: Aoyama 2015 - - Germline - - - - - Johan den Dunnen
+/. 1 _1i_6i c.(?_61-1)_(561+1_562-1)del r.? p.? - pathogenic (recessive) g.(24134814_24137225)_(24147084_?)del g.(23808324_23810735)_(23820594_?)del del ex(1_2)-6 - HMGCL_000018 - PubMed: Wang 1996 - - Germline - - - - - Johan den Dunnen
-?/. 1 - c.88C>T r.(?) p.(Pro30Ser) - likely benign g.24147056G>A g.23820566G>A HMGCL(NM_000191.2):c.88C>T (p.(Pro30Ser)) - HMGCL_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
+/. 6 2 c.109G>A r.(?), r.[109c>u,61_144del,61_252del] p.(Glu37Lys), p.[Glu37*,Val21_Lys48del,Val21_Gln84del] - pathogenic (recessive) g.24147035C>T g.23820545C>T - - HMGCL_000069 - PubMed: Casale 1998, PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 20 2 c.109G>T r.(?), r.[109c>u,61_144del] p.(Glu37*), p.(Glu37Ter), p.[Glu37*,Val21_Lys48del] ACMG pathogenic, pathogenic (recessive) g.24147035C>A g.23820545C>A E37X, HMGCL(NM_000191.3):c.109G>T (p.E37*) - HMGCL_000024 HMGCL activity 0.00, HMGCL activity 0.00 (compound heterozygous), HMGCL activity 0.08, 3 more items PubMed: Cardoso 2004, PubMed: Grünert 2017 PubMed: Muñoz-Bonet 2017 PubMed: Puisac 2013, 4 more items ClinVar-195033 rs763494292 CLASSIFICATION record, Germline yes - - - - Johan den Dunnen, VKGL-NL_VUmc, Miriam Erandi Reyna-Fabián
+?/. 1 2 c.112G>T r.(?) p.(Val38Phe) ACMG likely pathogenic (!) g.24147032C>A g.23820542C>A - - HMGCL_000071 1 more item - ClinVar-2075645 - Germline yes - - - - Miriam Erandi Reyna-Fabián
+/. 2 2 c.121C>T r.(?) p.(Arg41*) ACMG pathogenic (recessive) g.24147023G>A g.23820533G>A - - HMGCL_000023 Mitchel 1998:9463337, Pié 2007:17692550, Menao 2009:19177531, no variant 2nd chromosome PubMed: Mitchell 1998 ClinVar-553933 rs770225915 Germline yes - - - - Johan den Dunnen, Miriam Erandi Reyna-Fabián
+/. 60 - c.122G>A r.(?) p.(Arg41Gln) - pathogenic, pathogenic (recessive) g.24147022C>T g.23820532C>T HMGCL(NM_000191.3):c.122G>A (p.R41Q) - HMGCL_000004 no variant 2nd chromosome, VKGL data sharing initiative Nederland PubMed: Al-Sayed 2006, PubMed: Alfadhel 2022, Journal: Alfadhel 2022, PubMed: Mitchell 1998, 1 more item - - CLASSIFICATION record, Germline - 32/36 cases - - - Johan den Dunnen, VKGL-NL_Groningen, Muhammad Umair
+/. 1 - c.124G>A r.(?) p.(Asp42Asn) - pathogenic (recessive) g.24147020C>T - D42N - HMGCL_000044 - PubMed: Vargas 2008 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.124G>C r.(?) p.(Asp42His) - pathogenic (recessive) g.24147020C>G - - - HMGCL_000022 no variant 2nd chromosome PubMed: Mitchell 1998 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.125A>G r.(?) p.(Asp42Gly) - pathogenic (recessive) g.24147019T>C - - - HMGCL_000020 - PubMed: Mitchell 1998 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.126T>G r.(?) p.(Asp42Glu) - pathogenic (recessive) g.24147018A>C - - - HMGCL_000021 - PubMed: Mitchell 1998 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.137dup r.(?) p.(Asn46Lysfs*2) - pathogenic (recessive) g.24147010dup g.23820520dup 134-137insA - HMGCL_000016 - PubMed: Mitchell 1995 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.144G>T r.(?) p.(Lys48Asn) - pathogenic g.24147000C>A - g.144G>T - HMGCL_000043 2nd variant not reported PubMed: Carrasco 2007 - - Germline - - - - - Johan den Dunnen
+/. 1 2i_4i c.(144+1_145-1)_(348+1_349-1)del r.? p.? - pathogenic (recessive) g.(24140829_24143164)_(24144074_24146999)del g.(23814339_23816674)_(23817584_23820509)del del ex3-4 - HMGCL_000049 - PubMed: Koksal 2015 - - Germline - - - - - Johan den Dunnen
+/. 1 2i_6i c.(144+1_145-1)_(561+1_562-1)del r.? p.? - pathogenic (recessive) g.(24134814_24137225)_(24144074_24146999)del g.(23808324_23810735)_(23817584_23820509)del del ex3-6 - HMGCL_000017 - PubMed: Wang 1996 - - Germline - - - - - Johan den Dunnen
-?/. 1 - c.163G>C r.(?) p.(Val55Leu) - likely benign g.24144055C>G g.23817565C>G HMGCL(NM_000191.2):c.163G>C (p.V55L) - HMGCL_000009 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
+/. 6 - c.206_207del r.(?), r.206_207del p.(Ser69CysfsTer11), p.Ser69Cysfs*11 - pathogenic (recessive) g.24144015_24144016del g.23817525_23817526del - - HMGCL_000011 - PubMed: Alfadhel 2022, Journal: Alfadhel 2022, PubMed: Mitchell 1993 - - Germline yes - - - - Johan den Dunnen, Muhammad Umair
+/. 1 - c.225C>G r.(?) p.(Ser75Arg) - pathogenic (recessive) g.24143993G>C - - - HMGCL_000038 - PubMed: Casals 2003 - - Germline - - - - - Johan den Dunnen
+/. 1 3 c.230del r.(?) p.(Val77Glyfs*16) ACMG pathogenic (recessive) g.24143988del g.23817498del - - HMGCL_000072 1 more item - ClinVar-1685878 rs1638632303 Germline yes - - - - Miriam Erandi Reyna-Fabián
+?/. 1 3 c.233C>T r.(?) p.(Ser78Phe) ACMG likely pathogenic (recessive) g.24143985G>A g.23817495G>A - - HMGCL_000070 1 more item - ClinVar-2083770 rs754253328 Germline yes - - - - Miriam Erandi Reyna-Fabián
+/. 3 3 c.242G>A r.(?) p.(Trp81*), p.(Trp81Ter) - pathogenic (recessive) g.24143976C>T g.23817486C>T - - HMGCL_000052 paternal uniparental disomy of chromosome 1 PubMed: Aoyama 2015, PubMed: Menao 2009 - - Germline, Uniparental disomy, paternal allele - - - - - Johan den Dunnen
+/. 1 - c.252G>A r.145_252del p.Asn49_Gln84del - pathogenic (recessive) g.24143966C>T g.23817476C>T - - HMGCL_000068 - PubMed: Grunert 2017 - - Germline - - - - - Johan den Dunnen
+/. 1 3i c.252+1del r.145_252del p.Asn49_Gln84del - pathogenic (recessive) g.24143966del g.23817476del 252+1delG - HMGCL_000030 - PubMed: Muroi 2000 - - Germline - - - - - Johan den Dunnen
+/. 1 3i c.252+1G>A r.145_252del p.Asn49_Gln84del - pathogenic (recessive) g.24143965C>T - IVS3+1G>A - HMGCL_000047 - PubMed: Lin 2009 - - Germline - - - - - Johan den Dunnen
-/. 1 3i c.252+34= r.(?) p.? - benign g.24143932= g.23817442= - - HMGCL_000067 - PubMed: Menao 2009 - rs2076344 Germline - - - - - Johan den Dunnen
+/. 1 - c.272T>A r.(?) p.(Val91Asp) - pathogenic (recessive) g.24143241A>T g.23816751A>T - - HMGCL_000066 - PubMed: Grunert 2017 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.286C>T r.286c>u p.Gln96* - pathogenic (recessive) g.24143227G>A - - - HMGCL_000032 - PubMed: Funghini 2001 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.308_317dup r.(?) p.(Thr107ProfsTer48) - pathogenic (recessive) g.24143198_24143207dup g.23816708_23816717dup - - HMGCL_000065 - PubMed: Alfadhel 2022, Journal: Alfadhel 2022 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.323C>T r.(?) p.(Pro108Leu) - pathogenic (recessive) g.24143190G>A - - - HMGCL_000054 - PubMed: Grunert 2017 - - Germline - - - - - Johan den Dunnen
?/. 1 - c.344C>T r.(?) p.(Ala115Val) - VUS g.24143169G>A g.23816679G>A HMGCL(NM_000191.2):c.344C>T (p.A115V) - HMGCL_000005 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
?/. 2 - c.349-3C>A r.spl? p.? - VUS g.24140831G>T g.23814341G>T HMGCL(NM_000191.2):c.349-3C>A, HMGCL(NM_000191.3):c.349-3C>A - HMGCL_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden, VKGL-NL_Rotterdam
+/. 3 - c.374_375del r.(?) p.(Val125Aspfs*26), p.(Val125AspfsTer26) - pathogenic (recessive) g.24140802_24140803del g.23814312_23814313del 374_375delTC, c.374_375delTC - HMGCL_000041 - PubMed: Grunert 2017, PubMed: Zafeiriou 2007 - - Germline - - - - - Johan den Dunnen
+/. 1 5 c.425C>T r.(?) p.(Ser142Phe) - pathogenic (recessive) g.24140752G>A g.23814262G>A - - HMGCL_000064 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.434A>T r.433_561del p.Gln145_Glu187del - pathogenic (recessive) g.24140743T>A - A434T - HMGCL_000029 - PubMed: Muroi 2000 - - Germline - - - - - Johan den Dunnen
+/. 2 - c.493C>T r.(?) p.(Arg165Trp) - pathogenic (recessive) g.24140684G>A g.23814194G>A - - HMGCL_000063 - PubMed: Grunert 2017 - - Germline - - - - - Johan den Dunnen
+/. 2 - c.494G>A r.(?) p.(Arg165Gln) - pathogenic (recessive) g.24140683C>T - - - HMGCL_000045 - PubMed: Lin 2009, PubMed: Pierron 2010 - - De novo, Germline - - - - - Johan den Dunnen
+/. 1 5i c.497+4A>G r.[349_497del,349_561del] p.[Ala118Arfs*10,Val117_Glu187del] - pathogenic (recessive) g.24140676T>C g.23814186T>C - - HMGCL_000062 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 6 6 c.505_506del r.(?), r.[505_506del,498_561del,349_561del] p.(Ser169Leufs*8), p.[Ser169Leufs*8,Tyr167Serfs*27,Ala118_Val188del] ACMG pathogenic (recessive) g.24137283_24137284del g.23810793_23810794del 504_505delCT, V168fs(−2) - HMGCL_000019 HMGCL activity 0.07 (compound heterozygous), 1 more item PubMed: Cardoso 2004, PubMed: Casals 1997, PubMed: Vargas 2008 ClinVar-521753 rs764264834 Germline yes - - - - Johan den Dunnen, Miriam Erandi Reyna-Fabián
+/. 1 6 c.521G>A r.(?) p.(Cys174Tyr) - pathogenic (recessive) g.24137266C>T g.23810776C>T - - HMGCL_000061 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 1 6 c.559G>T r.(?) p.(Glu187Ter) - pathogenic (recessive) g.24137228C>A g.23810738C>A - - HMGCL_000060 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.561+1G>A r.spl p.? - pathogenic (recessive) g.24137225C>T - IVS6+1GA - HMGCL_000040 - PubMed: Al-Sayed 2006 - - Germline - 1/36 cases - - - Johan den Dunnen
+/. 1 6i c.562-1G>A r.(562_750del) p.(Val188_Gln250del) - pathogenic (recessive) g.24134814C>T g.23808324C>T IVS6-1G>A - HMGCL_000046 Fig.1C show other variant (654A>G) PubMed: Lin 2009 - - Germline - - - - - Johan den Dunnen
+/. 1 6i_7i c.(561+1_562-1)_(750+1_751-1)del r.562_750del p.Val188_Gln250del - pathogenic (recessive) g.(24131016_24134624)_(24134814_24137225)del g,(23804526_23808134)_(23808324_23810735)del ex del7 - HMGCL_000031 2.2 kb deletion PubMed: Muroi 2000 - - Germline - - - - - Johan den Dunnen
+/. 1 7 c.575T>C r.(?) p.(Phe192Ser) - pathogenic (recessive) g.24134800A>G g.23808310A>G - - HMGCL_000059 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 1 7 c.598A>T r.(?) p.(Ile200Phe) - pathogenic (recessive) g.24134777T>A g.23808287T>A - - HMGCL_000058 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.599T>A r.(?) p.(Ile200Asn) - pathogenic (recessive) g.24134776A>T g.23808286A>T - - HMGCL_000013 - PubMed: Alfadhel 2022, Journal: Alfadhel 2022 - - Germline - - - - - Muhammad Umair
+/. 1 - c.602C>A r.(?) p.(Ser201Tyr) - pathogenic (recessive) g.24134773G>T - - - HMGCL_000037 - PubMed: Casals 2003 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.608G>A r.(?) p.(Gly203Glu) - pathogenic (recessive) g.24134767C>T - - - HMGCL_000039 - PubMed: Mir 2006 - - Germline - - - - - Johan den Dunnen
+/. 2 - c.610G>A r.(?) p.(Asp204Asn) - pathogenic (recessive) g.24134765C>T - - - HMGCL_000036 HMGCL activity 0.00 (compound heterozygous) PubMed: Cardoso 2004, PubMed: Casals 2003 - - Germline - - - - - Johan den Dunnen
?/. 1 - c.650T>G r.(?) p.(Met217Arg) - VUS g.24134725A>C g.23808235A>C HMGCL(NM_000191.2):c.650T>G (p.(Met217Arg)) - HMGCL_000007 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
-/., -?/. 4 - c.654A>G r.(=), r.(?) p.(=), p.(Leu218=) - benign, likely benign g.24134721T>C g.23808231T>C HMGCL(NM_000191.3):c.654A>G (p.L218=) - HMGCL_000003 shown in Fig.1C (not reported), VKGL data sharing initiative Nederland PubMed: Lin 2009, PubMed: Pie 1997 - - CLASSIFICATION record, Germline - - - - - Johan den Dunnen, VKGL-NL_Groningen, VKGL-NL_Nijmegen
+/. 1 - c.658del r.(?) p.(Ala220LeufsTer27) - pathogenic (recessive) g.24134717del g.23808227del c.658_658delG - HMGCL_000057 - PubMed: Grunert 2017 - - Germline - - - - - Johan den Dunnen
-?/. 1 - c.663C>T r.(?) p.(Val221=) - likely benign g.24134712G>A - HMGCL(NM_000191.2):c.663C>T (p.V221=) - HMGCL_000010 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
+/. 1 - c.697C>G - p.His233Asp - NA g.24134678G>C - - - HMGCL_000034 functional analysis shows <0.01 specific activity PubMed: Roberts 1996 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.697_698delinsGC - p.His233Ala - NA g.24134677_24134678delinsGC - - - HMGCL_000035 functional analysis shows <0.01 specific activity PubMed: Roberts 1996 - - Germline - - - - - Johan den Dunnen
+/. 4 - c.698A>G -, r.(?), r.698a>g p.(His233Arg), p.His233Arg - NA, pathogenic (recessive) g.24134677T>C - A698G - HMGCL_000025 functional analysis shows <0.01 specific activity PubMed: Pospisilova 2003, PubMed: Roberts 1996, PubMed: Zapater 1998 - - Germline, In vitro (cloned) - - - - - Johan den Dunnen
-/. 1 - c.727G>A r.(?) p.(Ala243Thr) - benign g.24134648C>T - - - HMGCL_000053 - PubMed: Pie 1997 - - Germline - - - - - Johan den Dunnen
+/. 2 7i c.750+1G>A r.(?) p.? - pathogenic (recessive) g.24134624C>T g.23808134C>T - - HMGCL_000056 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
-?/. 1 - c.751-3T>C r.spl? p.? - likely benign g.24131018A>G g.23804528A>G HMGCL(NM_000191.2):c.751-3T>C - HMGCL_000015 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
+/. 1 - c.788T>C r.788u>c p.Leu263Pro - pathogenic (recessive) g.24130978A>G - T788C - HMGCL_000026 - PubMed: Zapater 1998 - - Germline - - - - - Johan den Dunnen
+/. 1 - c.796T>C r.(?) p.(Cys266Arg) - pathogenic (recessive) g.24130970A>G - 796C>T (C266R) - HMGCL_000042 - PubMed: Zafeiriou 2007 - - Germline - - - - - Johan den Dunnen
?/. 1 - c.805G>A r.(?) p.(Ala269Thr) - VUS g.24130961C>T g.23804471C>T HMGCL(NM_000191.3):c.805G>A (p.A269T) - HMGCL_000002 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Groningen
+/. 1 - c.820G>A r.(?) p.(Gly274Arg) - pathogenic (recessive) g.24130946C>T - - - HMGCL_000048 - PubMed: Pierron 2010 - - Germline - - - - - Johan den Dunnen
+/. 2 - c.835G>A r.835g>a p.Glu279Lys - pathogenic (recessive) g.24130931C>T - G835A - HMGCL_000027 - PubMed: Muroi 2000 - rs28934894 Germline - - - - - Johan den Dunnen
+/. 1 8 c.853del r.853del p.Leu285Ter - pathogenic (recessive) g.24130913del g.23804423del 853delC - HMGCL_000055 - PubMed: Menao 2009 - - Germline - - - - - Johan den Dunnen
+/. 7 8i c.876+1G>C r.spl, r.spl?, r.[751_876del,876_877ins[c;876+1_876+78]] p.?, p.[Met231_Thr292del,Gly393Leufs*18] - pathogenic, pathogenic (recessive) g.24130889C>G g.23804399C>G - - HMGCL_000014 VKGL data sharing initiative Nederland PubMed: Buesa 1996, PubMed: Grunert 2017, PubMed: Koling 2000, PubMed: Grunert 2017 - - CLASSIFICATION record, Germline - - - - - Johan den Dunnen, VKGL-NL_Nijmegen
+/. 6 - c.914_915del r.(?) p.(Arg41Gln), p.(Phe305Tyrfs*10), p.(Phe305TyrfsTer10) - pathogenic (recessive) g.24129017_24129018del g.23802527_23802528del 914_915delTT, F305fs(-2), g.913-15delTT - HMGCL_000012 study includes functional analysis variant PubMed: Al-Sayed 2006, PubMed: Alfadhel 2022, Journal: Alfadhel 2022, PubMed: Carrasco 2007, 1 more item - - Germline - 1/36 cases - - - Johan den Dunnen, Muhammad Umair
+/. 1 - c.922C>T r.922c>u p.Gln308* - pathogenic (recessive) g.24129009G>A - C922T - HMGCL_000028 - PubMed: Muroi 2000 - - Germline - - - - - Johan den Dunnen
?/. 1 - c.950A>G r.(?) p.(Lys317Arg) - VUS g.24128981T>C g.23802491T>C HMGCL(NM_000191.2):c.950A>G (p.(Lys317Arg)) - HMGCL_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
?/. 1 - c.*3474G>C r.(=) p.(=) - VUS g.24125479C>G - GALE(NM_000403.3):c.19G>C (p.V7L) - GALE_000011 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
+/. 1 - c.*4745C>T r.(=) p.(=) - pathogenic g.24124208G>A - - - GALE_000019 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Nijmegen
-?/. 1 - c.*5306C>T r.(=) p.(=) - likely benign g.24123647G>A - GALE(NM_000403.3):c.529-10C>T - GALE_000009 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
?/. 1 - c.*5525C>T r.(=) p.(=) - VUS g.24123428G>A - GALE(NM_001008216.2):c.647C>T (p.(Ala216Val)) - GALE_000020 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
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