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Variant: NM_005629.4(SLC6A8):c.26G>T (p.Gly9Val)

CA415075922

571505 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 7e44f106-9e73-4858-94c3-a84c52c65f60
Approved on: 2022-06-06
Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.26G>T
NM_005629.4(SLC6A8):c.26G>T (p.Gly9Val)
NC_000023.11:g.153688600G>T
CM000685.2:g.153688600G>T
NC_000023.10:g.152954055G>T
CM000685.1:g.152954055G>T
NC_000023.9:g.152607249G>T
NG_012016.1:g.5304G>T
NG_012016.2:g.5304G>T
ENST00000253122.10:c.26G>T
ENST00000253122.9:c.26G>T
ENST00000458354.5:c.-3+215C>A
ENST00000480693.1:n.64+215C>A
NM_001142805.1:c.26G>T
NM_005629.3:c.26G>T
NM_001142805.2:c.26G>T

Likely Benign

Met criteria codes 2
BS1 BP4

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.26G>T variant in SLC6A8 is a missense variant predicted to cause substitution of Glycine for Valine at amino acid 9 (p.Gly9Val). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00019 (14/74655 alleles) in the European population. Additionally, there are 5 hemizygotes in gnomAD v2.1.1, which is higher than the ClinGen CCDS VCEP’s threshold for BS1 (<5 hemizygotes in gnomAD). The computational predictor REVEL gives a score of 0.146 which is below the threshold of 0.25, evidence that does not predict a damaging effect on SLC6A8 function (PP3). To our knowledge, this variant has not been previously reported in affected individuals in the literature. There is a ClinVar entry for this variant (Variation ID:571505). In summary, this variant meets the criteria to be classified as Likely Benign for Creatine Transporter Deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): BS1, BP4. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is [0.00019] (14/74655 alleles) in the [European] population. Additionally, there are 5 hemizygotes in gnomADv2.1, which is higher than the ClinGen CCDS VCEP’s threshold for BS1 (<5 hemizygotes in gnomAD), and therefore meets this criterion
BP4
The computational predictor REVEL gives a score of [0.146] which is below the threshold of 0.25, evidence that does not predict a damaging effect on SLC6A8 function.
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