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 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.1714G>A (p.Val572Met)

CA10549625

449188 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 2cc6ed2d-738b-4e56-b234-d86b8505b1c3
Approved on: 2025-03-13
Published on: 2025-03-14

HGVS expressions

NM_005629.4:c.1714G>A
NM_005629.4(SLC6A8):c.1714G>A (p.Val572Met)
NC_000023.11:g.153694836G>A
CM000685.2:g.153694836G>A
NC_000023.10:g.152960291G>A
CM000685.1:g.152960291G>A
NC_000023.9:g.152613485G>A
NG_012016.1:g.11540G>A
NG_012016.2:g.11540G>A
ENST00000253122.10:c.1714G>A
ENST00000253122.9:c.1714G>A
ENST00000430077.6:c.1369G>A
ENST00000485324.1:n.2021G>A
NM_001142805.1:c.1684G>A
NM_001142806.1:c.1369G>A
NM_005629.3:c.1714G>A
NM_001142805.2:c.1684G>A
More

Likely Benign

Met criteria codes 1
BS2
Not Met criteria codes 4
BP4 PP3 PM2 BS1

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.1714G>A variant in SLC6A8 is a missense variant predicted to cause the substitution of a valine by a methionine at amino acid position 572 (p.Val572Met). 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 MAF) is 0.0000369 (33/894244 alleles, 12 hemizygotes) in the European (Non-Finnish) population. This MAF is greater than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.00002) but less than the ClinGen CCDS VCEP’s threshold for BS1 (>0.0002), such that neither of these criteria are met. There are 14 hemizygotes in gnomAD v4.1.0. (12 in the European non-Finnish, one in the "other" and one in the S. Asian population) (BS2). The computational predictor REVEL gives a score of 0.689, 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: 449188). Due to the presence of 14 hemizygotes in gnomAD v4.1.0, the consensus of the CCDS VCEP is to classify this variant as likely benign for creatine transporter deficiency, a severe, pediatric onset neurodevelopmental disorder. SLC6A8-specific ACMG/AMP criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): BS2. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on March 13, 2025)
Met criteria codes
BS2
There are 14 hemizygotes in gnomAD v4.1.0. (12 in the European non-Finnish, one in the "remaining" and one in the S. Asian population) (BS2).
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.689, 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. The computation predictor, SpliceAI, predicts no impact on splicing.
PP3
The computational predictor REVEL gives a score of 0.689, 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 minor allele frequency MAF) is 0.0000369 (33/894244 alleles, 12 hemizygotes) in the European (Non-Finnish) population. This MAF is greater than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.00002) but less than the ClinGen CCDS VCEP’s threshold for BS1 (>0.0002), such that neither of these criteria are met.
BS1
In gnomAD v4.1.0, the highest population minor allele frequency MAF) is 0.0000369 (33/894244 alleles, 12 hemizygotes) in the European (Non-Finnish) population. This MAF is greater than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.00002) but less than the ClinGen CCDS VCEP’s threshold for BS1 (>0.0002), such that neither of these criteria are met.
Curation History
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