SLC45A1 — 219 ClinVar variants
All ClinVar germline SLC45A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 100 flagged for review →
2 Conflicting · 11 Benign · 1 Benign/Likely benign · 69 Likely benign · 136 Uncertain significance
Full SLC45A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 100
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 85
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SLC45A1 p.Ala225Thr Uncertain significance Multiple submitters
-
SLC45A1 p.Arg670Gln
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Arg742Trp Uncertain significance Multiple submitters
- SLC45A1 p.Gly383Ser Uncertain significance Multiple submitters
- SLC45A1 p.Gly384Cys Uncertain significance Multiple submitters
-
SLC45A1 p.Gly393Asp
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Phe15Leu Uncertain significance Multiple submitters
-
SLC45A1 p.Phe272Leu
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
-
SLC45A1 p.Pro312Leu
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Ser209Leu Uncertain significance Multiple submitters
-
SLC45A1 p.Thr29Met
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
-
SLC45A1 p.Val490Met
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
-
SLC45A1 p.Val528Ile
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Ala207Pro Uncertain significance Single submitter
- SLC45A1 p.Ala207Val Uncertain significance Single submitter
- SLC45A1 p.Ala216Thr Uncertain significance Single submitter
- SLC45A1 p.Ala235Thr Uncertain significance Single submitter
- SLC45A1 p.Ala274Val Uncertain significance Single submitter
- SLC45A1 p.Ala365Thr Uncertain significance Single submitter
- SLC45A1 p.Ala458Val Uncertain significance Single submitter
- SLC45A1 p.Ala4Thr Uncertain significance Single submitter
- SLC45A1 p.Ala610Thr Uncertain significance Single submitter
- SLC45A1 p.Arg267Gln Uncertain significance Single submitter
- SLC45A1 p.Arg294Gln Uncertain significance Single submitter
- SLC45A1 p.Arg300Gln Uncertain significance Single submitter
-
SLC45A1 p.Arg37Leu
Uncertain significance
Single submitter
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Arg397Gly Uncertain significance Single submitter
-
SLC45A1 p.Arg413Cys
Uncertain significance
Single submitter
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Arg502Cys Uncertain significance Single submitter
- SLC45A1 p.Arg511Cys Uncertain significance Single submitter
- SLC45A1 p.Arg671Trp Uncertain significance Single submitter
- SLC45A1 p.Asn626Lys Uncertain significance Single submitter
- SLC45A1 p.Asn706Ser Uncertain significance Single submitter
- SLC45A1 p.Asp324Asn Uncertain significance Single submitter
- SLC45A1 p.Asp415Gly Uncertain significance Single submitter
- SLC45A1 p.Glu493Asp Uncertain significance Single submitter
- SLC45A1 p.Gly116Val Uncertain significance Single submitter
- SLC45A1 p.Gly179Val Uncertain significance Single submitter
- SLC45A1 p.Gly241Arg Uncertain significance Single submitter
- SLC45A1 p.Gly30Asp Uncertain significance Single submitter
- SLC45A1 p.Gly30Val Uncertain significance Single submitter
- SLC45A1 p.Gly321Val Uncertain significance Single submitter
- SLC45A1 p.Gly323Asp Uncertain significance Single submitter
- SLC45A1 p.Gly384Ser Uncertain significance Single submitter
- SLC45A1 p.Gly432Arg Uncertain significance Single submitter
- SLC45A1 p.Gly466Arg Uncertain significance Single submitter
- SLC45A1 p.Gly572Ser Uncertain significance Single submitter
- SLC45A1 p.Gly619Trp Uncertain significance Single submitter
- SLC45A1 p.Gly638Arg Uncertain significance Single submitter
- SLC45A1 p.Gly668Ser Uncertain significance Single submitter
- SLC45A1 p.Gly672Ser Uncertain significance Single submitter
- SLC45A1 p.Gly707Arg Uncertain significance Single submitter
- SLC45A1 p.Ile131Val Uncertain significance Single submitter
- SLC45A1 p.Ile635Thr Uncertain significance Single submitter
-
SLC45A1 p.Leu419Gln
Uncertain significance
Single submitter
intellectual developmental disorder with neuropsychiatric features
-
SLC45A1 p.Leu419Pro
Uncertain significance
Single submitter
intellectual developmental disorder with neuropsychiatric features
-
SLC45A1 p.Leu652Phe
Uncertain significance
Single submitter
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Leu746Met Uncertain significance Single submitter
- SLC45A1 p.Met519Val Uncertain significance Single submitter
- SLC45A1 p.Pro309Arg Uncertain significance Single submitter
- SLC45A1 p.Pro309Leu Uncertain significance Single submitter
- SLC45A1 p.Pro399Leu Uncertain significance Single submitter
- SLC45A1 p.Pro460Leu Uncertain significance Single submitter
- SLC45A1 p.Pro9Leu Uncertain significance Single submitter
- SLC45A1 p.Ser325Asn Uncertain significance Single submitter
- SLC45A1 p.Ser328Leu Uncertain significance Single submitter
- SLC45A1 p.Ser339Leu Uncertain significance Single submitter
- SLC45A1 p.Ser471Asn Uncertain significance Single submitter
- SLC45A1 p.Ser536Pro Uncertain significance Single submitter
- SLC45A1 p.Ser6Arg Uncertain significance Single submitter
- SLC45A1 p.Thr330Met Uncertain significance Single submitter
- SLC45A1 p.Tyr611Cys Uncertain significance Single submitter
- SLC45A1 p.Val125Met Uncertain significance Single submitter
- SLC45A1 p.Val185Met Uncertain significance Single submitter
-
SLC45A1 p.Val18Met
Uncertain significance
Single submitter
SLC45A1-related disorder
- SLC45A1 p.Val286Ala Uncertain significance Single submitter
- SLC45A1 p.Val28Asp Uncertain significance Single submitter
- SLC45A1 p.Val316Ile Uncertain significance Single submitter
- SLC45A1 p.Val376Ile Uncertain significance Single submitter
- SLC45A1 p.Val402Ile Uncertain significance Single submitter
- SLC45A1 p.Val552Met Uncertain significance Single submitter
- SLC45A1 p.Val694Leu Uncertain significance Single submitter
- SLC45A1 p.Val715Met Uncertain significance Single submitter
- SLC45A1 p.Val748Ile Uncertain significance Single submitter
- SLC45A1 p.Val748Phe Uncertain significance Single submitter
Predictors split 15
The independent predictors disagree with each other — read with care.
-
SLC45A1 p.Arg42Trp
Uncertain significance
Multiple submitters
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Ala181Thr Uncertain significance Single submitter
- SLC45A1 p.Ala610Ser Uncertain significance Single submitter
-
SLC45A1 p.Arg176Trp
Conflicting
Single submitter
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Asn475Lys Uncertain significance Single submitter
- SLC45A1 p.Asn65Asp Uncertain significance Single submitter
- SLC45A1 p.Cys517Arg Uncertain significance Single submitter
- SLC45A1 p.Ile485Val Uncertain significance Single submitter
-
SLC45A1 p.Ile56Thr
Uncertain significance
Single submitter
intellectual developmental disorder with neuropsychiatric features
- SLC45A1 p.Leu507Pro Uncertain significance Single submitter
- SLC45A1 p.Phe404Leu Uncertain significance Single submitter
- SLC45A1 p.Ser632Leu Uncertain significance Single submitter
- SLC45A1 p.Thr256Met Uncertain significance Single submitter
- SLC45A1 p.Thr345Lys Uncertain significance Single submitter
- SLC45A1 p.Tyr628Cys Uncertain significance Single submitter
All SLC45A1 variants
Conflicting classifications of pathogenicity 2
- p.Ala210Val Single submitter intellectual developmental disorder with neuropsychiatric features
- p.Arg176Trp Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
Benign 11
- c.*20C>T Multiple submitters intellectual developmental disorder with neuropsychiatric features
- p.Ala210= Multiple submitters
- p.Ala503Ser Multiple submitters intellectual developmental disorder with neuropsychiatric features
- p.Ala666= Multiple submitters
- p.Asp204= Multiple submitters
- p.Leu277= Multiple submitters intellectual developmental disorder with neuropsychiatric features
- p.Leu714= Multiple submitters
- p.Pro314= Multiple submitters intellectual developmental disorder with neuropsychiatric features
- p.Ser508= Multiple submitters
- p.Ser632= Multiple submitters
- p.Pro445= Single submitter intellectual developmental disorder with neuropsychiatric features
Benign/Likely benign 1
- p.Val200= Multiple submitters
Likely benign 69
- p.Ala736= Multiple submitters
- p.Arg294= Multiple submitters
- p.Asn706= Multiple submitters
- p.Asp409= Multiple submitters
- p.Gly242= Multiple submitters
- p.Pro60= Multiple submitters
- p.Ser375= Multiple submitters
- p.Thr256= Multiple submitters
- p.Thr618= Multiple submitters
- c.1443+5C>G Single submitter
- c.1597+10C>T Single submitter
- c.715+10C>T Single submitter
- p.Ala165= Single submitter
- p.Ala261= Single submitter
- p.Ala274= Single submitter
- p.Ala463= Single submitter
- p.Ala503= Single submitter
- p.Ala565= Single submitter
- p.Ala666Val Single submitter
- p.Arg413His Single submitter
- p.Arg472= Single submitter
- p.Arg511His Single submitter
- p.Arg742Gln Single submitter
- p.Asn747= Single submitter
- p.Asn90= Single submitter
- p.Asp220= Single submitter
- p.Asp667= Single submitter
- p.Cys92= Single submitter
- p.Glu504= Single submitter
- p.Gly533= Single submitter
- p.His234= Single submitter
- p.Ile131= Single submitter
- p.Ile609= Single submitter
- p.Leu117= Single submitter
- p.Leu140= Single submitter
- p.Leu14Phe Single submitter
- p.Leu240= Single submitter
- p.Leu310= Single submitter
- p.Leu535= Single submitter
- p.Leu616= Single submitter
- p.Phe614= Single submitter
- p.Pro118= Single submitter
- p.Pro292= Single submitter
- p.Pro309= Single submitter
- p.Pro327= Single submitter
- p.Pro67= Single submitter
- p.Ser278= Single submitter
- p.Ser32= Single submitter
- p.Ser34= Single submitter
- p.Ser428= Single submitter
- p.Ser83= Single submitter
- p.Thr281= Single submitter
- p.Thr370= Single submitter
- p.Thr497= Single submitter
- p.Tyr246= Single submitter
- p.Tyr270= Single submitter
- p.Tyr637= Single submitter
- p.Val248= Single submitter
- p.Val279Ile Single submitter
- p.Val509Met Single submitter
- p.Val603Ile Single submitter
- c.1444-9del No assertion criteria SLC45A1-related disorder
- c.1774+6C>T No assertion criteria SLC45A1-related disorder
- p.Ala302= No assertion criteria SLC45A1-related disorder
- p.Pro3= No assertion criteria SLC45A1-related disorder
- p.Pro312= No assertion criteria SLC45A1-related disorder
- p.Pro62= No assertion criteria SLC45A1-related disorder
- p.Ser59= No assertion criteria SLC45A1-related disorder
- p.Val247= No assertion criteria SLC45A1-related disorder
Uncertain significance 136
- p.Ala225Thr Multiple submitters ⚠
- p.Arg42Trp Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Arg670Gln Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Arg742Trp Multiple submitters ⚠
- p.Gly383Ser Multiple submitters ⚠
- p.Gly384Cys Multiple submitters ⚠
- p.Gly393Asp Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Phe15Leu Multiple submitters ⚠
- p.Phe272Leu Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Pro312Leu Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Pro340Leu Multiple submitters SLC45A1-related disorder
- p.Ser209Leu Multiple submitters ⚠
- p.Thr29Met Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Val490Met Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- p.Val528Ile Multiple submitters intellectual developmental disorder with neuropsychiatric features ⚠
- c.1443+1G>A Single submitter
- p.Ala181Ser Single submitter
- p.Ala181Thr Single submitter ⚠
- p.Ala207Pro Single submitter ⚠
- p.Ala207Thr Single submitter
- p.Ala207Val Single submitter ⚠
- p.Ala216Thr Single submitter ⚠
- p.Ala235Thr Single submitter ⚠
- p.Ala261Val Single submitter
- p.Ala274Val Single submitter ⚠
- p.Ala365Thr Single submitter ⚠
- p.Ala458Val Single submitter ⚠
- p.Ala4Thr Single submitter ⚠
- p.Ala522Val Single submitter
- p.Ala584Thr Single submitter
- p.Ala610Ser Single submitter ⚠
- p.Ala610Thr Single submitter ⚠
- p.Ala613Thr Single submitter
- p.Arg146Gln Single submitter
- p.Arg267Gln Single submitter ⚠
- p.Arg294Gln Single submitter ⚠
- p.Arg300Gln Single submitter ⚠
- p.Arg300Trp Single submitter
- p.Arg37Leu Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
- p.Arg397Gly Single submitter ⚠
- p.Arg413Cys Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
- p.Arg502Cys Single submitter ⚠
- p.Arg511Cys Single submitter ⚠
- p.Arg57Cys Single submitter
- p.Arg57His Single submitter intellectual developmental disorder with neuropsychiatric features
- p.Arg670Trp Single submitter
- p.Arg671Trp Single submitter ⚠
- p.Asn475Lys Single submitter ⚠
- p.Asn626Lys Single submitter ⚠
- p.Asn65Asp Single submitter ⚠
- p.Asn706Ser Single submitter ⚠
- p.Asp119Asn Single submitter
- p.Asp324Asn Single submitter ⚠
- p.Asp415Gly Single submitter ⚠
- p.Cys517Arg Single submitter ⚠
- p.Glu493Asp Single submitter ⚠
- p.Glu501Lys Single submitter
- p.Glu550Lys Single submitter
- p.Glu598Gln Single submitter
- p.Gly116Val Single submitter ⚠
- p.Gly179Val Single submitter ⚠
- p.Gly241Arg Single submitter ⚠
- p.Gly30Asp Single submitter ⚠
- p.Gly30Val Single submitter ⚠
- p.Gly321Val Single submitter ⚠
- p.Gly323Asp Single submitter ⚠
- p.Gly384Ser Single submitter ⚠
- p.Gly432Arg Single submitter ⚠
- p.Gly466Arg Single submitter ⚠
- p.Gly489Ser Single submitter
- p.Gly572Ser Single submitter ⚠
- p.Gly619Trp Single submitter ⚠
- p.Gly638Arg Single submitter ⚠
- p.Gly668Ser Single submitter ⚠
- p.Gly672Ser Single submitter ⚠
- p.Gly707Arg Single submitter ⚠
- p.Gly91Ser Single submitter
- p.His38Gln Single submitter intellectual developmental disorder with neuropsychiatric features
- p.Ile131Val Single submitter ⚠
- p.Ile485Val Single submitter ⚠
- p.Ile56Thr Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
- p.Ile635Thr Single submitter ⚠
- p.Ile677Val Single submitter
- p.Leu419Gln Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
- p.Leu419Pro Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
- p.Leu507Pro Single submitter ⚠
- p.Leu601Phe Single submitter
- p.Leu652Phe Single submitter intellectual developmental disorder with neuropsychiatric features ⚠
- p.Leu746Met Single submitter ⚠
- p.Lys47Thr Single submitter
- p.Met519Val Single submitter ⚠
- p.Phe404Leu Single submitter ⚠
- p.Phe589Leu Single submitter
- p.Pro309Arg Single submitter ⚠
- p.Pro309Leu Single submitter ⚠
- p.Pro315Leu Single submitter
- p.Pro399Leu Single submitter ⚠
- p.Pro408Arg Single submitter
- p.Pro460Leu Single submitter ⚠
- p.Pro9Leu Single submitter ⚠
- p.Ser287Arg Single submitter
- p.Ser313Cys Single submitter intellectual developmental disorder with neuropsychiatric features
- p.Ser325Asn Single submitter ⚠
- p.Ser328Leu Single submitter ⚠
- p.Ser339Leu Single submitter ⚠
- p.Ser394Arg Single submitter
- p.Ser471Asn Single submitter ⚠
- p.Ser536Pro Single submitter ⚠
- p.Ser59Cys Single submitter
- p.Ser602Arg Single submitter
- p.Ser632Leu Single submitter ⚠
- p.Ser6Arg Single submitter ⚠
- p.Thr256Met Single submitter ⚠
- p.Thr330Met Single submitter ⚠
- p.Thr345Lys Single submitter ⚠
- p.Thr643Ser Single submitter
- p.Tyr611Cys Single submitter ⚠
- p.Tyr628Cys Single submitter ⚠
- p.Val125Met Single submitter ⚠
- p.Val185Met Single submitter ⚠
- p.Val18Met Single submitter SLC45A1-related disorder ⚠
- p.Val197Met Single submitter
- p.Val247Met Single submitter
- p.Val248Leu Single submitter intellectual developmental disorder with neuropsychiatric features
- p.Val282Leu Single submitter
- p.Val286Ala Single submitter ⚠
- p.Val28Asp Single submitter ⚠
- p.Val316Ile Single submitter ⚠
- p.Val376Ile Single submitter ⚠
- p.Val402Ile Single submitter ⚠
- p.Val552Met Single submitter ⚠
- p.Val694Leu Single submitter ⚠
- p.Val702Met Single submitter
- p.Val715Met Single submitter ⚠
- p.Val748Ile Single submitter ⚠
- p.Val748Phe Single submitter ⚠