Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001142805.2:c.1269_1279del

CA2582121421

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: b8bbf64c-58d4-4843-9f3e-0e01e3acb175
Approved on: 2024-03-25
Published on: 2024-03-25

HGVS expressions

NM_001142805.2:c.1269_1279del
NC_000023.11:g.153694174_153694184del
CM000685.2:g.153694174_153694184del
NC_000023.10:g.152959629_152959639del
CM000685.1:g.152959629_152959639del
NC_000023.9:g.152612823_152612833del
NG_012016.1:g.10878_10888del
NG_012016.2:g.10878_10888del
ENST00000253122.10:c.1299_1309del
ENST00000253122.9:c.1299_1309del
ENST00000413787.1:c.258-30_258-20del
ENST00000430077.6:c.954_964del
ENST00000442457.1:c.353_363del
ENST00000485324.1:n.1444_1454del
NM_001142805.1:c.1269_1279del
NM_001142806.1:c.954_964del
NM_005629.3:c.1299_1309del
NM_005629.4:c.1299_1309del

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4

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.1299_1309del variant in SLC6A8 is a frameshift variant predicted to cause a premature stop codon in biologically relevant exon 9/13 leading to nonsense mediated decay in a gene in which loss of function is an established disease mechanism (p.Pro434LeufsTer27) (PVS1). This variant has been reported in one hemizygous male individual with elevated urinary creatine/creatinine (PMID: 23644449) (PP4). The variant is absent in gnomAD v2.1.1. (PM2_Supporting). In summary, this variant meets criteria to be classified as pathogenic for creatine transporter deficiency. SLC6A8-specific criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): PVS1, PM2_Supporting, PP4. (Classification approved by the ClinGen CCDS VCEP on March 25, 2024)
Met criteria codes
PM2_Supporting
The variant is absent in gnomAD v2.1.1. (PM2_Supporting).
PVS1
The NM_005629.4:c.1299_1309del variant in SLC6A8 is a frameshift variant predicted to cause a premature stop codon in biologically relevant exon 9/13 leading to nonsense mediated decay in a gene in which loss of function is an established disease mechanism (p.Pro434LeufsTer27) (PVS1).
PP4
This variant has been reported in one hemizygous male individual with elevated urinary creatine/creatinine (PMID: 23644449) (PP4).
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