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  • No ClinVar Id was directly found from the curated document


Variant: NM_001142805.2:c.1116_1120dup

CA2579985607

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 39ac7632-eadd-46df-8007-b03daf68e463
Approved on: 2023-08-08
Published on: 2024-03-29

HGVS expressions

NM_001142805.2:c.1116_1120dup
NC_000023.11:g.153693909_153693913dup
CM000685.2:g.153693909_153693913dup
NC_000023.10:g.152959364_152959368dup
CM000685.1:g.152959364_152959368dup
NC_000023.9:g.152612558_152612562dup
NG_012016.1:g.10613_10617dup
NG_012016.2:g.10613_10617dup
ENST00000253122.10:c.1146_1150dup
ENST00000253122.9:c.1146_1150dup
ENST00000413787.1:c.258-295_258-291dup
ENST00000430077.6:c.801_805dup
ENST00000442457.1:c.200_204dup
ENST00000457723.1:c.130_134dup
ENST00000467402.1:n.245_249dup
ENST00000485324.1:n.1179_1183dup
NM_001142805.1:c.1116_1120dup
NM_001142806.1:c.801_805dup
NM_005629.3:c.1146_1150dup
NM_005629.4:c.1146_1150dup

Pathogenic

Met criteria codes 4
PM2_Supporting PP4 PM6 PVS1

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.1146_1150dup (p.Leu384ArgfsTer14) (a.k.a. NC_000023.11:g.153693909_153693913dup) in SLC6A8 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 8 of 13, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). A male patient with clinical features consistent with creatine transporter deficiency, hemizygous for the variant, was reported to have had elevated urine creatine levels on two occasions (PMID: 27096572) (PP4). His mother did not appear to carry the variant; maternity was not confirmed (PM6). The variant is absent in gnomAD v2.1.1. (PM2_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for creatine transporter deficiency. SLC6A8-specific ACMG/AMP criteria applied, as specified by the ClinGen CCDS Variant Curation Expert Panel (Specifications Version 1.1.0): PVS1, PM6, PP4, PM2_Supporting. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on August 8, 2023).
Met criteria codes
PM2_Supporting
The variant is absent in gnomAD v2.1.1. (PM2_Supporting).
PP4
A male patient with clinical features consistent with creatine transporter deficiency was reported to have had elevated urine creatine levels on two occassions (PMID: 27096572) (PP4)
PM6
The mother of a male who is hemizygous for the variant did not appear to carry the variant (maternity was not confirmed) (PM6).
PVS1
The NM_005629.4:c.1146_1150dup (p.Leu384ArgfsTer14) (a.k.a. NC_000023.11:g.153693909_153693913dup) in SLC6A8 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 8 of 13, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
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