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NM_005629.4(SLC6A8):c.1255-35G>A AND Creatine transporter deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 28, 2024
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:
RCV003991445.1

Allele description [Variation Report for NM_005629.4(SLC6A8):c.1255-35G>A]

NM_005629.4(SLC6A8):c.1255-35G>A

Gene:
SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_005629.4(SLC6A8):c.1255-35G>A
Other names:
NM_001142805.2:c.1225-35G>A
HGVS:
  • NC_000023.11:g.153694095G>A
  • NG_012016.2:g.10799G>A
  • NM_001142805.2:c.1225-35G>A
  • NM_001142806.1:c.910-35G>A
  • NM_005629.4:c.1255-35G>AMANE SELECT
  • NC_000023.10:g.152959550G>A
Molecular consequence:
  • NM_001142805.2:c.1225-35G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001142806.1:c.910-35G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_005629.4:c.1255-35G>A - intron variant - [Sequence Ontology: SO:0001627]

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
SCV004809053ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen_CCDS_ACMG_Specifications_SLC6A8_v1.1)		Uncertain significance
(Mar 28, 2024) 		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, SCV004809053.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_005629.4:c.1255-35G>A variant in SLC6A8 is an intronic variant affecting a nucleotide within the consensus splice site of intron 8. This variant has been reported as a novel variant in one individual undergoing genetic testing for suspected X-linked intellectual disability (PMID: 15154114), without further specification; thus PP4 does not apply. The variant is absent in gnomAD v2.1.1. (PM2_Supporting). The computational predictors SpliceAI and varSEAK predict that this variant does not impact splicing (BP4). 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): PM2_Supporting, BP4. Curation Expert Panel on March 28, 2024)

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

Last Updated: Apr 15, 2024