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NC_000023.11:g.153693904GGGCC[3] AND Creatine transporter deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 8, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003991450.1

Allele description [Variation Report for NC_000023.11:g.153693904GGGCC[3]]

NC_000023.11:g.153693904GGGCC[3]

Gene:
SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NC_000023.11:g.153693904GGGCC[3]
Other names:
NM_001142805.2:c.1116_1120dup
HGVS:
  • NC_000023.11:g.153693904GGGCC[3]
  • NG_012016.2:g.10608GGGCC[3]
  • NC_000023.10:g.152959359GGGCC[3]
  • NC_000023.11:g.153693909_153693913dup

Condition(s)

Name:
Creatine transporter deficiency (CCDS1)
Synonyms:
Creatine deficiency, X-linked; Mental retardation , X-linked with seizures, short stature and midface hypoplasia; Mental retardation , X-linked, with creatine transport deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010305; MedGen: C1845862; Orphanet: 52503; OMIM: 300352

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004809060ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen_CCDS_ACMG_Specifications_SLC6A8_v1.1)		Pathogenic
(Aug 8, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen, SCV004809060.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 15, 2024