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Variant: NM_005629.4(SLC6A8):c.53_137delinsCCGTGT (p.Lys18fs)

CA658799891

533702 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 87a150ee-003c-4846-93f5-b7c2ad446032
Approved on: 2022-06-06
Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.53_137delinsCCGTGT
NM_005629.4(SLC6A8):c.53_137delinsCCGTGT (p.Lys18fs)
NC_000023.11:g.153688627_153688711delinsCCGTGT
CM000685.2:g.153688627_153688711delinsCCGTGT
NC_000023.10:g.152954082_152954166delinsCCGTGT
CM000685.1:g.152954082_152954166delinsCCGTGT
NC_000023.9:g.152607276_152607360delinsCCGTGT
NG_012016.1:g.5331_5415delinsCCGTGT
NG_012016.2:g.5331_5415delinsCCGTGT
ENST00000253122.10:c.53_137delinsCCGTGT
ENST00000253122.9:c.53_137delinsCCGTGT
ENST00000458354.5:c.-3+104_-3+188delinsACACGG
ENST00000480693.1:n.64+104_64+188delinsACACGG
NM_001142805.1:c.53_137delinsCCGTGT
NM_005629.3:c.53_137delinsCCGTGT
NM_001142805.2:c.53_137delinsCCGTGT
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Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 2
PVS1 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(SLC6A8):c.53_137delinsCCGTGT (p.Lys18fs) variant in SLC6A8 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 1/13, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant is absent in population databases (PM2_Supporting), and to our current knowledge has not been reported in affected individuals in the literature. There is a ClinVar entry for this variant (Variation ID:533702). In summary, this variant meets the criteria to be classified as Likely Pathogenic 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 1.0): PVS1, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
PVS1
The NM_005629.4(SLC6A8):c.53_137delinsCCGTGT (p.Lys18fs) variant in SLC6A8 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 1/13, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism.
PM2_Supporting
This variant is absent in gnomAD (v2.1)
Curation History
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