NM_001128225.3(SLC39A13):c.234G>A (p.Val78=) AND Ehlers-Danlos syndrome, spondylocheirodysplastic type

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 4, 2021
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:: RCV002010557.4

Allele description [Variation Report for NM_001128225.3(SLC39A13):c.234G>A (p.Val78=)]

NM_001128225.3(SLC39A13):c.234G>A (p.Val78=)

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.234G>A (p.Val78=)

HGVS:

NC_000011.10:g.47410328G>A
NG_017073.1:g.6834G>A
NM_001128225.3:c.234G>AMANE SELECT
NM_001330245.2:c.234G>A
NM_152264.5:c.234G>A
NP_001121697.2:p.Val78=
NP_001317174.2:p.Val78=
NP_689477.3:p.Val78=
NC_000011.9:g.47431879G>A
NR_134854.1:n.500G>A

Links:

dbSNP: rs140298838

NCBI 1000 Genomes Browser:

rs140298838

Molecular consequence:

NR_134854.1:n.500G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001128225.3:c.234G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330245.2:c.234G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_152264.5:c.234G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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

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PREDICTED: Homo sapiens mitogen-activated protein kinase kinase kinase 20 (MAP3K...
PREDICTED: Homo sapiens mitogen-activated protein kinase kinase kinase 20 (MAP3K20), transcript variant X3, mRNA
gi|2462574313|ref|XM_054342554.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002297277	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 2021)	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

SCV002297277

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 2021)

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, SCV002297277.3

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. This variant has not been reported in the literature in individuals affected with SLC39A13-related conditions. This variant is present in population databases (rs140298838, ExAC 0.003%). This sequence change affects codon 78 of the SLC39A13 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SLC39A13 protein.

#	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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