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Variant: NM_005629.4(SLC6A8):c.259G>A (p.Gly87Arg)

CA256012

11700 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: f7ed3567-7588-4422-8abd-3a935cec7f43

HGVS expressions

NM_005629.4:c.259G>A
NM_005629.4(SLC6A8):c.259G>A (p.Gly87Arg)
NC_000023.11:g.153688833G>A
CM000685.2:g.153688833G>A
NC_000023.10:g.152954288G>A
CM000685.1:g.152954288G>A
NC_000023.9:g.152607482G>A
NG_012016.1:g.5537G>A
NG_012016.2:g.5537G>A
ENST00000253122.10:c.259G>A
ENST00000253122.9:c.259G>A
ENST00000458354.5:c.-21C>T
ENST00000476466.1:n.111G>A
ENST00000480693.1:n.46C>T
NM_001142805.1:c.259G>A
NM_005629.3:c.259G>A
NM_001142805.2:c.259G>A

Uncertain Significance

Met criteria codes 3
PM2_Supporting PS3_Supporting PP3
Not Met criteria codes 2
PS1 PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4:c.259G>A variant in SLC6A8 is a missense variant predicted to cause substitution of glycine by arginine at amino acid 87 (p.Gly87Arg). This variant is absent in population databases (PM2_Supporting) and has been described in the literature in an individual for whom biochemical testing could not be performed (PMID: 15154114). The computational predictor REVEL gives a score of 0.961 which is above the thresholds predicting a damaging (>0.75) impact on SLC6A8 function (PP3). When fibroblasts deficient for this SLC6A8 variant were grown in the presence of a physiological Cr concentration (25uM), the average creatine uptake was just above the detection limit, whereas in the control fibroblasts it was significantly higher (PMID: 17465020) (PS3_Supporting). There is a ClinVar entry for this variant (Variation ID:11700). 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 Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PP3, PS3_Supporting, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP, July 13, 2023)
Met criteria codes
PM2_Supporting
Variant not seen in gnomAD
PS3_Supporting
When SLC6A8-deficient fibroblasts were grown in the presence of a physiological Cr concentration (25uM), the average creatine uptake was just above the detection limit, whereas in the control fibroblasts it was significantly higher (PMID: 17465020).
PP3
REVEL score for this variant is 0.961 (threshold of 0.75). So, PP3 is met.
Not Met criteria codes
PS1
Not applicable for this variant
PP4
This variant was reprted in a patient with X-linked disability; no biochemical or MRS analyses were performed (PMID: 15154114).
Approved on: 2023-08-24
Published on: 2023-08-24
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