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Variant: NM_001142805.2:c.1351A>G

CA415087081

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 3cb15110-f40d-405f-8a95-5bf40bef9087
Approved on: 2024-03-28
Published on: 2024-03-28

HGVS expressions

NM_001142805.2:c.1351A>G
NC_000023.11:g.153694256A>G
CM000685.2:g.153694256A>G
NC_000023.10:g.152959711A>G
CM000685.1:g.152959711A>G
NC_000023.9:g.152612905A>G
NG_012016.1:g.10960A>G
NG_012016.2:g.10960A>G
ENST00000253122.10:c.1381A>G
ENST00000253122.9:c.1381A>G
ENST00000413787.1:c.310A>G
ENST00000430077.6:c.1036A>G
ENST00000442457.1:c.435A>G
ENST00000485324.1:n.1526A>G
NM_001142805.1:c.1351A>G
NM_001142806.1:c.1036A>G
NM_005629.3:c.1381A>G
NM_005629.4:c.1381A>G

Uncertain Significance

Met criteria codes 2
PS3_Supporting PM2_Supporting
Not Met criteria codes 2
BP4 PP3

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.1381A>G variant in SLC6A8 is a missense variant that is predicted to lead to the substitution of a methionine for a valine at amino acid position 461 (p.Met461Val). This variant has not been reported in the published literature in individuals with creatine transporter deficiency. This variant was reported to result in reduced (<10% of wild-type) creatine transport activity in SLC6A8 deficient fibroblasts (PMID: 22281021) (PS3_Supporting). The variant is absent in gnomAD v2.1.1. (PM2_Supporting). The computational predictor REVEL gives a score of 0.713 which is neither above the threshold of 0.75 for PP3 nor below the threshold of 0.2 (BP4), such that neither PP3 nor BP4 applies. 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): PS3_Supporting, PM2_Supporting. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on March 28, 2024)
Met criteria codes
PS3_Supporting
This variant was reported to result in reduced (<10% of wild-type) creatine transport activity in SLC6A8 deficient fibroblasts (PMID: 22281021) (PS3_Supporting).
PM2_Supporting
The variant is absent in gnomAD v2.1.1. (PM2_Supporting).
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.713 which is neither above the threshold of 0.75 for PP3 nor below the threshold of 0.2 (BP4), such that neither PP3 nor BP4 applies.
PP3
The computational predictor REVEL gives a score of 0.713 which is neither above the threshold of 0.75 for PP3 nor below the threshold of 0.2 (BP4), such that neither PP3 nor BP4 applies.
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