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.283G>A (p.Val95Ile)

CA10549177

449185 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 0411cb9d-fe98-4cdd-8a5d-279df65c5225
Approved on: 2024-11-08
Published on: 2024-11-13

HGVS expressions

NM_005629.4:c.283G>A
NM_005629.4(SLC6A8):c.283G>A (p.Val95Ile)
NC_000023.11:g.153690395G>A
CM000685.2:g.153690395G>A
NC_000023.10:g.152955850G>A
CM000685.1:g.152955850G>A
NC_000023.9:g.152609044G>A
NG_012016.1:g.7099G>A
NG_012016.2:g.7099G>A
ENST00000253122.10:c.283G>A
ENST00000675713.1:n.37G>A
ENST00000253122.9:c.283G>A
ENST00000430077.6:c.-63G>A
ENST00000476466.1:n.135G>A
NM_001142805.1:c.283G>A
NM_001142806.1:c.-63G>A
NM_005629.3:c.283G>A
NM_001142805.2:c.283G>A
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Uncertain Significance

Not Met criteria codes 4
BS1 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.283G>A variant in SLC6A8 is a missense variant predicted to cause a substitution of a valine by an isoleucine at amino acid position 95 (p.Val95Ile). This variant has not been reported in the published literature in individuals with creatine transporter deficiency. In gnomAD v2.1.1, the highest population minor allele frequency is 0.00005 (4/78678 alleles, 2 hemizygotes) in the European (Non-Finnish) population, which 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. The computational predictor REVEL gives a score of 0.644, 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: 449185, one-star review status), with conflicting interpretations of pathogenicity (one submitter: uncertain significance; two submitters: likely benign). In summary, this variant meets criteria to be classified as a variant of uncertain significance for creatine transporter deficiency. SLC6A8-specific 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 November 8, 2024)
Not Met criteria codes
BS1
In gnomAD v2.1.1, the highest population minor allele frequency is 0.00005 (4/78678 alleles, 0 hemizygotes) in the European (Non-Finnish) population, which 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.
BP4
The computational predictor REVEL gives a score of 0.644, 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.
PP3
The computational predictor REVEL gives a score of 0.644, 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 v2.1.1, the highest population minor allele frequency is 0.00005 (4/78678 alleles, 2 hemizygotes) in the European (Non-Finnish) population, which 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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