The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: SLC6A8 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_005629.4(SLC6A8):c.1778A>G (p.His593Arg)

CA10549662

465144 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: b20114db-a663-4dfe-9c60-7a672cf3e8a0
Approved on: 2025-03-18
Published on: 2025-03-20

HGVS expressions

NM_005629.4:c.1778A>G
NM_005629.4(SLC6A8):c.1778A>G (p.His593Arg)
NC_000023.11:g.153695084A>G
CM000685.2:g.153695084A>G
NC_000023.10:g.152960539A>G
CM000685.1:g.152960539A>G
NC_000023.9:g.152613733A>G
NG_012016.1:g.11788A>G
NG_012016.2:g.11788A>G
ENST00000253122.10:c.1778A>G
ENST00000253122.9:c.1778A>G
ENST00000430077.6:c.1433A>G
ENST00000485324.1:n.2085A>G
NM_001142805.1:c.1748A>G
NM_001142806.1:c.1433A>G
NM_005629.3:c.1778A>G
NM_001142805.2:c.1748A>G
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Benign

Met criteria codes 3
BS1 BS2 BP4

Evidence Links 0

Expert Panel

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:c.1778A>G variant in SLC6A8 is a missense variant predicted to cause the substitution of a histidine by an arginine at amino acid position 593 (p.His593Arg). To our knowledge, this variant has not been reported in the literature and no functional studies are available. In gnomAD v4.1.0., the highest population minor allele frequency is 0.0004421 (20/45238 alleles; 2 homozygotes, 0 hemizygotes) in the Admixed American population. This MAF is higher than the ClinGen CCDS VCEP's threshold for BS1 (>0.0002), meeting this criterion (BS1). Overall, across all populations, there are 3 homozygotes and 7 hemizygotes in gnomAD v4.1.0. (BS2). The computational predictor REVEL gives a score of 0.133 suggesting that the variant has no impact on protein function. SpliceAI predicts no impact on splicing (BP4). There is a ClinVar entry for this variant (Variation ID: 465144). In summary, this variant meets criteria to be classified as benign for creatine transporter deficiency. SLC6A8-specific ACMG/AMP criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): BS1, BS2, BP4. (Classification approved by the ClinGen Cerebral Creatine Deficiencies Variant Curation Expert Panel on March 18, 2025)
Met criteria codes
BS1
In gnomAD v4.1.0., the highest population minor allele frequency is 0.0004421 (20/45238 alleles; 2 homozygotes, 0 hemizygotes) in the Admixed American population. This MAF is higher than the ClinGen CCDS VCEP's threshold for BS1 (>0.0002), meeting this criterion.
BS2
Overall, there are 3 homozygotes and 7 hemizygotes in gnomAD v4.1.0. (BS2)
BP4
The computational predictor REVEL gives a score of 0.133, which does not suggest that the variant has an impact on protein function. SpliceAI predicts no impact on splicing (BP4).
Curation History
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