The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_005629.4(SLC6A8):c.48C>A (p.Asp16Glu)

CA16609138

392671 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: b5af5632-dfea-4aee-ab45-dcd830141a0f
Approved on: 2022-06-06
Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.48C>A
NM_005629.4(SLC6A8):c.48C>A (p.Asp16Glu)
NC_000023.11:g.153688622C>A
CM000685.2:g.153688622C>A
NC_000023.10:g.152954077C>A
CM000685.1:g.152954077C>A
NC_000023.9:g.152607271C>A
NG_012016.1:g.5326C>A
NG_012016.2:g.5326C>A
ENST00000253122.10:c.48C>A
ENST00000253122.9:c.48C>A
ENST00000458354.5:c.-3+193G>T
ENST00000480693.1:n.64+193G>T
NM_001142805.1:c.48C>A
NM_005629.3:c.48C>A
NM_001142805.2:c.48C>A

Uncertain Significance

Met criteria codes 2
BP4 PM2_Supporting

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4:c.48C>A variant in SLC6A8 is a missense variant predicted to result in substitution of aspartate by glutamate at amino acid 16 (p.Asp16Glu). The variant is absent in gnomAD v2.1.1, although low coverage is noted (PM2_Supporting). The computational predictor REVEL gives a score of 0.123, evidence that does not predict a damaging effect on SLC6A8 function (BP4). To our knowledge, this variant has not been reported in any patients with creatine transporter deficiency in the literature. There is a ClinVar entry for this variant (Variation ID: 392671). In summary, this variant meets the 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 LSD VCEP (specifications version 1.1.0): PM2_Supporting, BP4. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.123, evidence that does not predict a damaging effect on SLC6A8 function (BP4).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (note low coverage) (PM2_Supporting).
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