SLC25A3 — 222 ClinVar variants
All ClinVar germline SLC25A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 62 flagged for review →
6 Pathogenic · 1 Pathogenic/Likely pathogenic · 4 Likely pathogenic · 5 Conflicting · 18 Benign · 3 Benign/Likely benign · 102 Likely benign · 83 Uncertain significance
Full SLC25A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 62
Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.
Predictors lean, ClinVar uncertain 46
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SLC25A3 p.Ala180Val Uncertain significance Multiple submitters
- SLC25A3 p.Ala220Val Uncertain significance Multiple submitters
-
SLC25A3 p.Arg239Cys
Uncertain significance
Multiple submitters
cardiomyopathy-hypotonia-lactic acidosis syndrome
- SLC25A3 p.Arg253Cys Uncertain significance Multiple submitters
- SLC25A3 p.Asn155Thr Uncertain significance Multiple submitters
- SLC25A3 p.Gly25Asp Uncertain significance Multiple submitters
- SLC25A3 p.Gly35Arg Uncertain significance Multiple submitters
- SLC25A3 p.His18Tyr Uncertain significance Multiple submitters
- SLC25A3 p.His23Gln Uncertain significance Multiple submitters
- SLC25A3 p.Ile278Val Uncertain significance Multiple submitters
-
SLC25A3 p.Met182Val
Uncertain significance
Multiple submitters
cardiomyopathy-hypotonia-lactic acidosis syndrome
-
SLC25A3 p.Pro17Ala
Uncertain significance
Multiple submitters
cardiomyopathy-hypotonia-lactic acidosis syndrome
- SLC25A3 p.Ser254Asn Uncertain significance Multiple submitters
- SLC25A3 p.Val22Gly Uncertain significance Multiple submitters
- SLC25A3 p.Val310Ile Uncertain significance Multiple submitters
- SLC25A3 p.Val335Met Uncertain significance Multiple submitters
- SLC25A3 p.Ala277Val Uncertain significance Single submitter
- SLC25A3 p.Arg160His Uncertain significance Single submitter
- SLC25A3 p.Arg253His Uncertain significance Single submitter
- SLC25A3 p.Arg41Pro Uncertain significance Single submitter
-
SLC25A3 p.Asn12His
Uncertain significance
Single submitter
cardiomyopathy-hypotonia-lactic acidosis syndrome
- SLC25A3 p.Asn149Ser Uncertain significance Single submitter
- SLC25A3 p.Asn155Asp Uncertain significance Single submitter
- SLC25A3 p.Glu260Gly Uncertain significance Single submitter
- SLC25A3 p.Glu351Asp Uncertain significance Single submitter
- SLC25A3 p.Gly117Cys Uncertain significance Single submitter
- SLC25A3 p.Gly27Arg Uncertain significance Single submitter
- SLC25A3 p.Gly309Ser Uncertain significance Single submitter
- SLC25A3 p.Ile271Val Uncertain significance Single submitter
- SLC25A3 p.Leu19Arg Uncertain significance Single submitter
- SLC25A3 p.Leu222Phe Uncertain significance Single submitter
- SLC25A3 p.Leu341Arg Uncertain significance Single submitter
- SLC25A3 p.Leu8Val Uncertain significance Single submitter
- SLC25A3 p.Lys120Glu Uncertain significance Single submitter
- SLC25A3 p.Lys186Glu Uncertain significance Single submitter
- SLC25A3 p.Lys217Glu Uncertain significance Single submitter
- SLC25A3 p.Lys356Gln Uncertain significance Single submitter
- SLC25A3 p.Phe266Leu Uncertain significance Single submitter
- SLC25A3 p.Phe2Val Uncertain significance Single submitter
- SLC25A3 p.Phe64Leu Uncertain significance Single submitter
- SLC25A3 p.Pro13Leu Uncertain significance Single submitter
- SLC25A3 p.Pro346Leu Uncertain significance Single submitter
- SLC25A3 p.Ser4Phe Uncertain significance Single submitter
- SLC25A3 p.Tyr338Cys Uncertain significance Single submitter
- SLC25A3 p.Tyr59Cys Uncertain significance Single submitter
- SLC25A3 p.Val264Leu Uncertain significance Single submitter
Predictors split 16
The independent predictors disagree with each other — read with care.
- SLC25A3 p.Ile102Met Uncertain significance Multiple submitters
- SLC25A3 p.Ala196Gly Uncertain significance Single submitter
- SLC25A3 p.Ala214Val Uncertain significance Single submitter
- SLC25A3 p.Arg116Cys Uncertain significance Single submitter
- SLC25A3 p.Arg116His Uncertain significance Single submitter
- SLC25A3 p.Arg343His Uncertain significance Single submitter
- SLC25A3 p.Asn12Lys Uncertain significance Single submitter
- SLC25A3 p.Glu351Lys Uncertain significance Single submitter
- SLC25A3 p.Ile318Met Uncertain significance Single submitter
- SLC25A3 p.Leu357Val Uncertain significance Single submitter
- SLC25A3 p.Phe2Leu Uncertain significance Single submitter
- SLC25A3 p.Phe339Leu Uncertain significance Single submitter
- SLC25A3 p.Pro345Ala Uncertain significance Single submitter
- SLC25A3 p.Ser297Gly Uncertain significance Single submitter
- SLC25A3 p.Tyr338Ser Uncertain significance Single submitter
- SLC25A3 p.Val289Ala Uncertain significance Single submitter
All SLC25A3 variants
Pathogenic 6
- p.Arg188Ter Single submitter
- p.Phe2fs Single submitter
- p.Tyr207_Lys208delinsTer Single submitter
- p.Gly295_Ser299delinsGlnIlePro No assertion criteria cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Gly72Glu No assertion criteria cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Leu199Trp No assertion criteria cardiomyopathy-hypotonia-lactic acidosis syndrome
Pathogenic/Likely pathogenic 1
- c.158-303A>G Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
Likely pathogenic 4
- c.158-1_164del Single submitter
- c.158-1G>C Single submitter
- c.280-1G>C Single submitter
- c.642-2A>G Single submitter
Conflicting classifications of pathogenicity 5
- c.642-4C>T Single submitter
- p.Asn104= Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Gly25= Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Leu21= Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Val286= Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
Benign 18
- c.157+241T>C Multiple submitters
- c.459+92T>C Multiple submitters
- c.460-236C>T Multiple submitters
- c.642-109A>G Multiple submitters
- c.642-90C>T Multiple submitters
- c.-78G>A Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*102C>A Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*211T>A Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*221T>G Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Leu146= Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Leu199= Multiple submitters
- c.158-5_158-2del Single submitter
- c.459+31del Single submitter
- c.641+171C>G Single submitter
- c.814+227C>T Single submitter
- c.814+249G>A Single submitter
- c.925+18dup Single submitter
- c.-38C>G Single submitter
Benign/Likely benign 3
- c.925+4G>A Multiple submitters
- c.-92G>A Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Tyr157= Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
Likely benign 102
- c.280-16C>T Multiple submitters
- c.460-36G>A Multiple submitters
- c.460-85G>A Multiple submitters
- c.641+7A>G Multiple submitters
- c.926-11G>A Multiple submitters
- p.Ala178= Multiple submitters
- p.Ala6= Multiple submitters
- p.Arg92= Multiple submitters
- p.Leu19= Multiple submitters
- p.Leu222= Multiple submitters
- p.Phe143= Multiple submitters
- p.Pro228= Multiple submitters
- p.Val310= Multiple submitters
- p.Val82= Multiple submitters
- c.157+10G>A Single submitter
- c.157+13C>A Single submitter
- c.157+18C>T Single submitter
- c.157+19C>T Single submitter
- c.157+20A>G Single submitter
- c.157+71C>G Single submitter
- c.158-307T>C Single submitter
- c.158-314T>C Single submitter
- c.279+292A>T Single submitter
- c.280-133del Single submitter
- c.280-17T>C Single submitter
- c.280-272C>T Single submitter
- c.459+16T>C Single submitter
- c.459+32G>C Single submitter
- c.460-177T>C Single submitter
- c.460-6T>C Single submitter
- c.460-70A>G Single submitter
- c.460-7A>G Single submitter
- c.460-97A>G Single submitter
- c.641+11A>T Single submitter
- c.641+18A>C Single submitter
- c.641+20_641+25del Single submitter
- c.641+221T>C Single submitter
- c.641+228G>A Single submitter
- c.641+234A>G Single submitter
- c.641+75_641+77dup Single submitter
- c.642-10G>C Single submitter
- c.642-13_642-12del Single submitter
- c.642-13C>T Single submitter
- c.642-145A>G Single submitter
- c.814+12T>G Single submitter
- c.814+15G>C Single submitter
- c.814+20C>G Single submitter
- c.814+302dup Single submitter
- c.814+34T>C Single submitter
- c.925+11del Single submitter
- c.925+16T>C Single submitter
- c.926-13C>G Single submitter
- c.-258G>A Single submitter
- c.-4-21C>T Single submitter
- c.-5+17C>A Single submitter
- c.-5+20C>T Single submitter
- c.-74C>T Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*208T>C Single submitter
- c.*3A>G Single submitter
- p.Ala119= Single submitter
- p.Ala166= Single submitter
- p.Ala235= Single submitter
- p.Ala49= Single submitter
- p.Ala50= Single submitter
- p.Ala61Val Single submitter
- p.Arg30= Single submitter
- p.Arg42= Single submitter
- p.Asn12= Single submitter
- p.Asp28= Single submitter
- p.Asp58= Single submitter
- p.Gln190= Single submitter
- p.Gln328= Single submitter
- p.Gln97= Single submitter
- p.Glu112= Single submitter
- p.Glu172= Single submitter
- p.Glu53= Single submitter
- p.Gly138= Single submitter
- p.Gly211= Single submitter
- p.Gly27= Single submitter
- p.Gly295= Single submitter
- p.Gly35= Single submitter
- p.His7= Single submitter
- p.Ile319= Single submitter
- p.Leu151= Single submitter
- p.Leu163= Single submitter
- p.Leu244= Single submitter
- p.Leu314= Single submitter
- p.Leu341= Single submitter
- p.Leu8= Single submitter
- p.Lys136= Single submitter
- p.Pro124= Single submitter
- p.Pro350= Single submitter
- p.Pro43Ser Single submitter
- p.Ser130= Single submitter
- p.Ser3= Single submitter
- p.Ser334= Single submitter
- p.Ser4= Single submitter
- p.Thr125= Single submitter
- p.Thr37= Single submitter
- p.Tyr195= Single submitter
- p.Val335= Single submitter
- p.Val337= Single submitter
Uncertain significance 83
- c.814+5G>T Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Ala180Val Multiple submitters ⚠
- p.Ala220Val Multiple submitters ⚠
- p.Arg239Cys Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome ⚠
- p.Arg253Cys Multiple submitters ⚠
- p.Asn155Thr Multiple submitters ⚠
- p.Gly25Asp Multiple submitters ⚠
- p.Gly35Arg Multiple submitters ⚠
- p.His18Tyr Multiple submitters ⚠
- p.His23Gln Multiple submitters ⚠
- p.Ile102Met Multiple submitters ⚠
- p.Ile278Val Multiple submitters ⚠
- p.Met182Val Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome ⚠
- p.Pro17Ala Multiple submitters cardiomyopathy-hypotonia-lactic acidosis syndrome ⚠
- p.Ser254Asn Multiple submitters ⚠
- p.Val22Gly Multiple submitters ⚠
- p.Val310Ile Multiple submitters ⚠
- p.Val335Met Multiple submitters ⚠
- c.158-301C>G Single submitter
- c.280-6A>G Single submitter
- c.814+4C>T Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.-120G>C Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.-38C>T Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.-4-7C>T Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.-61G>T Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.-69G>A Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*254A>G Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*255T>G Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*296G>T Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*316A>G Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*411T>C Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*429C>G Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- c.*94T>C Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Ala196Gly Single submitter ⚠
- p.Ala214Val Single submitter ⚠
- p.Ala277Val Single submitter ⚠
- p.Arg116Cys Single submitter ⚠
- p.Arg116His Single submitter ⚠
- p.Arg160His Single submitter ⚠
- p.Arg253His Single submitter ⚠
- p.Arg340= Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Arg343His Single submitter ⚠
- p.Arg41Pro Single submitter ⚠
- p.Asn12His Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome ⚠
- p.Asn12Lys Single submitter ⚠
- p.Asn149Ser Single submitter ⚠
- p.Asn155Asp Single submitter ⚠
- p.Glu260Gly Single submitter ⚠
- p.Glu351Asp Single submitter ⚠
- p.Glu351Lys Single submitter ⚠
- p.Gly117Cys Single submitter ⚠
- p.Gly27Arg Single submitter ⚠
- p.Gly309Ser Single submitter ⚠
- p.Ile271Val Single submitter ⚠
- p.Ile318Met Single submitter ⚠
- p.Leu19Arg Single submitter ⚠
- p.Leu222Phe Single submitter ⚠
- p.Leu341Arg Single submitter ⚠
- p.Leu357Val Single submitter ⚠
- p.Leu8Val Single submitter ⚠
- p.Lys120Glu Single submitter ⚠
- p.Lys186Glu Single submitter ⚠
- p.Lys217Glu Single submitter ⚠
- p.Lys356Gln Single submitter ⚠
- p.Met131Thr Single submitter
- p.Phe266Leu Single submitter ⚠
- p.Phe2Leu Single submitter ⚠
- p.Phe2Val Single submitter ⚠
- p.Phe339Leu Single submitter ⚠
- p.Phe64Leu Single submitter ⚠
- p.Pro13Leu Single submitter ⚠
- p.Pro17Leu Single submitter
- p.Pro345Ala Single submitter ⚠
- p.Pro346Leu Single submitter ⚠
- p.Ser297Gly Single submitter ⚠
- p.Ser4Phe Single submitter ⚠
- p.Tyr216= Single submitter cardiomyopathy-hypotonia-lactic acidosis syndrome
- p.Tyr338Cys Single submitter ⚠
- p.Tyr338Ser Single submitter ⚠
- p.Tyr59Cys Single submitter ⚠
- p.Val264Leu Single submitter ⚠
- p.Val287Ile Single submitter
- p.Val289Ala Single submitter ⚠