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.87G>C (p.Gly29=)

CA16608764

380589 (ClinVar)

Gene: SLC6A8

Condition: creatine transporter deficiency

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 5b2fb3d4-769c-46d9-801b-9ea6e23f448b

Approved on: 2022-06-06

Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.87G>C

NM_005629.4(SLC6A8):c.87G>C (p.Gly29=)

NC_000023.11:g.153688661G>C

CM000685.2:g.153688661G>C

NC_000023.10:g.152954116G>C

CM000685.1:g.152954116G>C

NC_000023.9:g.152607310G>C

NG_012016.1:g.5365G>C

NG_012016.2:g.5365G>C

ENST00000253122.10:c.87G>C

ENST00000253122.9:c.87G>C

ENST00000458354.5:c.-3+154C>G

ENST00000480693.1:n.64+154C>G

NM_001142805.1:c.87G>C

NM_005629.3:c.87G>C

NM_001142805.2:c.87G>C

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

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.87G>C (p.Gly29=) variant in SLC6A8 is a synonymous single nucleotide variant that does not change the amino acid sequence at this position. In gnomAD v2.1.1, the highest population minor allele frequency is 0.005489 (62/11296 alleles) in the European population, with 10 hemizygotes present. The presence of 10 hemizygotes in the gnomAD dataset meets BA1 standalone criteria for Creatine Transporter Deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (<10 hemizygotes in population database). This variant has not been previously reported in affected individuals in the literature. There is a ClinVar entry for this variant (Variation ID:380589). 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 1.0): BA1. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).

BA1

In gnomAD v2.1.1, the highest population minor allele frequency is 0.005489 (62/11296 alleles) in the European population, with 10 hemizygotes present. The presence of 10 hemizygotes in the gnomAD dataset meets BA1 standalone criteria for Creatine Transporter Deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel.

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