Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_005629.4(SLC6A8):c.1162G>A (p.Ala388Thr)

CA10549443

436771 (ClinVar)

Gene: SLC6A8

Condition: creatine transporter deficiency

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 79b7be5f-ce88-4161-a6df-707def707253

Approved on: 2023-02-23

Published on: 2024-02-11

HGVS expressions

NM_005629.4:c.1162G>A

NM_005629.4(SLC6A8):c.1162G>A (p.Ala388Thr)

NC_000023.11:g.153693925G>A

CM000685.2:g.153693925G>A

NC_000023.10:g.152959380G>A

CM000685.1:g.152959380G>A

NC_000023.9:g.152612574G>A

NG_012016.1:g.10629G>A

NG_012016.2:g.10629G>A

ENST00000253122.10:c.1162G>A

ENST00000253122.9:c.1162G>A

ENST00000413787.1:c.258-279G>A

ENST00000430077.6:c.817G>A

ENST00000442457.1:c.216G>A

ENST00000457723.1:c.146G>A

ENST00000467402.1:n.261G>A

ENST00000485324.1:n.1195G>A

NM_001142805.1:c.1132G>A

NM_001142806.1:c.817G>A

NM_005629.3:c.1162G>A

NM_001142805.2:c.1132G>A

Benign

BA1

Evidence Links 0

Expert Panel

Cerebral Creatine Deficiency Syndromes VCEP

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC6A8 Version 1.1.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Cerebral Creatine Deficiency Syndromes VCEP

The NM_005629.4(SLC6A8):c.1162G>A (p.Ala388Thr) variant in SLC6A8 is a missense variant predicted to cause substitution of Threonine for Alanine at amino acid 338 (p.Ala338Thr). There is a ClinVar entry for this variant (Variation ID:436771). This variant is found with an allele frequency of 0.003854 in gnomADv2.1.1 with 17 hemizygotes present in that population database. Given the presence of >10 hemizygotes in gnomADv2.1.1 and an allele frequency >0.002, the stand alone benign criteria BA1 is applicable for this variant. In summary, this variant meets the criteria to be classified as Benign for Creatine Transporter Deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0; ; classification approved Feb 23, 2023): BA1

BA1

This variant is found with an allele frequency of 0.003854 in gnomADv2.1.1 with 17 hemizygotes present in that population database. Given the presence of >10 hemizygotes in gnomADv2.1.1, and an allele frequency >0.002, the stand alone benign criteria BA1 is applicable for this variant.

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