NM_001128225.3(SLC39A13):c.118C>T (p.Arg40Trp) AND Ehlers-Danlos syndrome, spondylocheirodysplastic type

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 2023
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:: RCV000807005.7

Allele description [Variation Report for NM_001128225.3(SLC39A13):c.118C>T (p.Arg40Trp)]

NM_001128225.3(SLC39A13):c.118C>T (p.Arg40Trp)

Gene:

SLC39A13:solute carrier family 39 member 13 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_001128225.3(SLC39A13):c.118C>T (p.Arg40Trp)

HGVS:

NC_000011.10:g.47410212C>T
NG_017073.1:g.6718C>T
NM_001128225.3:c.118C>TMANE SELECT
NM_001330245.2:c.118C>T
NM_152264.5:c.118C>T
NP_001121697.2:p.Arg40Trp
NP_001317174.2:p.Arg40Trp
NP_689477.2:p.Arg40Trp
NP_689477.3:p.Arg40Trp
NC_000011.9:g.47431763C>T
NM_152264.4:c.118C>T
NR_134854.1:n.384C>T

Protein change:

R40W

Links:

dbSNP: rs368796707

NCBI 1000 Genomes Browser:

rs368796707

Molecular consequence:

NM_001128225.3:c.118C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330245.2:c.118C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152264.5:c.118C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_134854.1:n.384C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Ehlers-Danlos syndrome, spondylocheirodysplastic type
Synonyms:: Spondylocheirodysplasia, Ehlers-Danlos syndrome-like; EHLERS-DANLOS SYNDROME, SPONDYLODYSPLASTIC TYPE, 3
Identifiers:: MONDO: MONDO:0012873; MedGen: C2676510; Orphanet: 157965; OMIM: 612350

Recent activity

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protein phosphatase 2A, regulatory subunit B (PR 53), isoform CRA_a [Mus musculu...
protein phosphatase 2A, regulatory subunit B (PR 53), isoform CRA_a [Mus musculus]
gi|148676525|gb|EDL08472.1||gnl|WGS |mCP19560

Protein
LOC128924492 [Mus musculus]
LOC128924492 [Mus musculus]
Gene ID:128924492

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000947030	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 2023)	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

SCV000947030

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 2023)

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, SCV000947030.4

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 40 of the SLC39A13 protein (p.Arg40Trp). This variant is present in population databases (rs368796707, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SLC39A13-related conditions. ClinVar contains an entry for this variant (Variation ID: 651607). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The tryptophan amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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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