NM_005629.4(SLC6A8):c.1214T>C (p.Leu405Pro) AND Creatine transporter deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 19, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001319400.8

Allele description [Variation Report for NM_005629.4(SLC6A8):c.1214T>C (p.Leu405Pro)]

NM_005629.4(SLC6A8):c.1214T>C (p.Leu405Pro)

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.1214T>C (p.Leu405Pro)

HGVS:

NC_000023.11:g.153693977T>C
NG_012016.2:g.10681T>C
NM_001142805.2:c.1184T>C
NM_001142806.1:c.869T>C
NM_005629.3:c.1214T>C
NM_005629.4:c.1214T>CMANE SELECT
NP_001136277.1:p.Leu395Pro
NP_001136278.1:p.Leu290Pro
NP_005620.1:p.Leu405Pro
NC_000023.10:g.152959432T>C
NG_012016.1:g.10681T>C

Protein change:

L290P

Links:

dbSNP: rs2091472678

NCBI 1000 Genomes Browser:

rs2091472678

Molecular consequence:

NM_001142805.2:c.1184T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142806.1:c.869T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005629.4:c.1214T>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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MIMAG Metagenome-assembled Genome sample from Patescibacteria group bacterium
MIMAG Metagenome-assembled Genome sample from Patescibacteria group bacterium

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001510142	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 19, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001510142

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 19, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001510142.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SLC6A8-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 405 of the SLC6A8 protein (p.Leu405Pro). The leucine residue is highly conserved and there is a moderate physicochemical difference between leucine and proline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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