NM_015335.5(MED13L):c.6545A>G (p.Asn2182Ser) AND Transposition of the great arteries, dextro-looped 1

Clinical significance:Uncertain significance (Last evaluated: Apr 20, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000532583.1

Allele description [Variation Report for NM_015335.5(MED13L):c.6545A>G (p.Asn2182Ser)]

NM_015335.5(MED13L):c.6545A>G (p.Asn2182Ser)

Gene:
MED13L:mediator complex subunit 13L [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.21
Genomic location:
Preferred name:
NM_015335.5(MED13L):c.6545A>G (p.Asn2182Ser)
HGVS:
  • NC_000012.12:g.115961354T>C
  • NG_023366.1:g.320833A>G
  • NM_015335.4:c.6545A>G
  • NM_015335.5:c.6545A>GMANE SELECT
  • NP_056150.1:p.Asn2182Ser
  • NP_056150.1:p.Asn2182Ser
  • NC_000012.11:g.116399159T>C
Protein change:
N2182S
Links:
dbSNP: rs762926166
NCBI 1000 Genomes Browser:
rs762926166
Molecular consequence:
  • NM_015335.4:c.6545A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015335.5:c.6545A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Transposition of the great arteries, dextro-looped 1 (DTGA)
Identifiers:
MONDO: MONDO:0012128; MedGen: C1837341; Orphanet: 860; OMIM: 608808

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000639023Invitaecriteria provided, single submitter
Uncertain significance
(Apr 20, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000639023.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces asparagine with serine at codon 2182 of the MED13L protein (p.Asn2182Ser). The asparagine residue is highly conserved and there is a small physicochemical difference between asparagine and serine. This variant is present in population databases (rs762926166, ExAC 0.08%) but has not been reported in the literature in individuals with a MED13L-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, this variant is a rare missense change with uncertain impact on protein function. Because it is found in the population at an appreciable frequency, this variant is not anticipated to cause disease. However, the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 25, 2021

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