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NM_005629.4(SLC6A8):c.1249A>C (p.Ser417Arg) AND Creatine transporter deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 24, 2019
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001253759.2

Allele description [Variation Report for NM_005629.4(SLC6A8):c.1249A>C (p.Ser417Arg)]

NM_005629.4(SLC6A8):c.1249A>C (p.Ser417Arg)

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.1249A>C (p.Ser417Arg)
HGVS:
  • NC_000023.11:g.153694012A>C
  • NG_012016.2:g.10716A>C
  • NM_001142805.2:c.1219A>C
  • NM_001142806.1:c.904A>C
  • NM_005629.4:c.1249A>CMANE SELECT
  • NP_001136277.1:p.Ser407Arg
  • NP_001136278.1:p.Ser302Arg
  • NP_005620.1:p.Ser417Arg
  • NC_000023.10:g.152959467A>C
  • NG_012016.1:g.10716A>C
  • NM_005629.3:c.1249A>C
  • p.Ser417Arg
Protein change:
S302R
Links:
dbSNP: rs2091472899
NCBI 1000 Genomes Browser:
rs2091472899
Molecular consequence:
  • NM_001142805.2:c.1219A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142806.1:c.904A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005629.4:c.1249A>C - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001427059Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Uncertain significance
(May 24, 2019) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Clinical Genomics Laboratory, Stanford Medicine, SCV001427059.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The p.Ser417Arg variant in the SLC6A8 gene was identified de novo in this individual, but has not been previously reported in association with disease. A different missense variant at the same residue, p.Ser417Asn, has been reported in ClinVar by another clinical laboratory (ClinVar accession: SCV000516297.4). This p.Ser417Asn variant has been observed de novo in an unrelated, unpublished proband with a neurodevelopmental condition, however full clinical details were not available for consideration by our laboratory (GeneDx, personal communication, 5/21/19). The p.Ser417Arg variant detected in this individual was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Computational tools predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Ser417Arg variant is uncertain. Additional information is needed to resolve the significance of this variant [ACMG evidence codes used: PS2_supporting; PM2; PP3].

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

Last Updated: Jul 7, 2024