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.1512G>T (p.Met504Ile)

CA10549554

1342107 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: a73ff7aa-4d26-4fc3-8c1d-8d1c434d5600
Approved on: 2025-05-20
Published on: 2025-05-20

HGVS expressions

NM_005629.4:c.1512G>T
NM_005629.4(SLC6A8):c.1512G>T (p.Met504Ile)
NC_000023.11:g.153694549G>T
CM000685.2:g.153694549G>T
NC_000023.10:g.152960004G>T
CM000685.1:g.152960004G>T
NC_000023.9:g.152613198G>T
NG_012016.1:g.11253G>T
NG_012016.2:g.11253G>T
ENST00000253122.10:c.1512G>T
ENST00000253122.9:c.1512G>T
ENST00000413787.1:c.441G>T
ENST00000430077.6:c.1167G>T
ENST00000485324.1:n.1819G>T
NM_001142805.1:c.1482G>T
NM_001142806.1:c.1167G>T
NM_005629.3:c.1512G>T
NM_001142805.2:c.1482G>T
More

Uncertain Significance

Not Met criteria codes 4
BS2 BP4 PP3 PM2

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.1512G>T variant in SLC6A8 is a missense variant predicted to cause the substitution of a methionine by an isoleucine at amino acid position 504 (p.Met504Ile). 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 allele frequency is 0.000006708 (6/894470 alleles, 1 hemizygote) in the European (non-Finnish) population. While this MAF meets the threshold for PM2_Supporting, the criterion is not met due to the presence of a hemizygote. Although a hemizygote is present in gnomAD v4.1.0. this is insufficient for application of BS2 (2 or more hemizygotes required; BS2 not met). The computational predictor REVEL gives a score of 0.349, which is less than the ClinGen CCDS VCEP’s threshold for PP3 (>0.75) but greater than the ClinGen CCDS VCEP’s threshold for BP4 (<0.2), such that neither of these criteria are met. There is a ClinVar entry for this variant (Variation ID: 1342107). In summary, this variant meets criteria to be classified as a variant of uncertain significance for creatine transporter deficiency. SLC6A8-specific ACMG/AMP criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): no criteria met. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on May 20, 2025)
Not Met criteria codes
BS2
One hemizygote in gnomAD v4.1.0. (insufficient for application of BS2; 2 or more hemizygotes required).
BP4
The computational predictor REVEL gives a score of 0.349, which is less than the ClinGen CCDS VCEP’s threshold for PP3 (>0.75) but greater than the ClinGen CCDS VCEP’s threshold for BP4 (<0.2), such that neither of these criteria are met. SpliceAI suggest that the variant has no impact on splicing (all scores <0.1).
PP3
The computational predictor REVEL gives a score of 0.349, which is less than the ClinGen CCDS VCEP’s threshold for PP3 (>0.75) but greater than the ClinGen CCDS VCEP’s threshold for BP4 (<0.2), such that neither of these criteria are met.
PM2
In gnomAD v4.1.0, the highest population allele frequency is 0.000006708 (6/894470 alleles, 1 hemizygote) in the European (non-Finnish) population. While this MAF meets the threshold for PM2_Supporting, the criterion is not met due to the presence of a hemizygote.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.