NM_018834.6(MATR3):c.85C>T (p.Leu29Phe) AND Amyotrophic lateral sclerosis 21

Clinical significance:Uncertain significance (Last evaluated: Feb 22, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001339294.1

Allele description [Variation Report for NM_018834.6(MATR3):c.85C>T (p.Leu29Phe)]

NM_018834.6(MATR3):c.85C>T (p.Leu29Phe)

Gene:
MATR3:matrin 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.2
Genomic location:
Preferred name:
NM_018834.6(MATR3):c.85C>T (p.Leu29Phe)
HGVS:
  • NC_000005.10:g.139307500C>T
  • NG_012846.1:g.38398C>T
  • NM_001194954.2:c.85C>T
  • NM_001194955.2:c.85C>T
  • NM_001194956.2:c.49-7175C>T
  • NM_001282278.2:c.-102-7175C>T
  • NM_018834.6:c.85C>TMANE SELECT
  • NM_199189.3:c.85C>T
  • NP_001181883.1:p.Leu29Phe
  • NP_001181884.1:p.Leu29Phe
  • NP_061322.2:p.Leu29Phe
  • NP_954659.1:p.Leu29Phe
  • NC_000005.9:g.138643189C>T
Protein change:
L29F
Links:
dbSNP: rs1754770320
NCBI 1000 Genomes Browser:
rs1754770320
Molecular consequence:
  • NM_001194956.2:c.49-7175C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282278.2:c.-102-7175C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001194954.2:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001194955.2:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018834.6:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_199189.3:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Amyotrophic lateral sclerosis 21 (ALS21)
Synonyms:
VOCAL CORD AND PHARYNGEAL DYSFUNCTION WITH DISTAL MYOPATHY; Myopathy, distal, 2
Identifiers:
MONDO: MONDO:0011632; MedGen: C3807521; Orphanet: 600; Orphanet: 803; OMIM: 606070

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001533027Invitaecriteria provided, single submitter
Uncertain significance
(Feb 22, 2020)
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, SCV001533027.1

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

Description

This sequence change replaces leucine with phenylalanine at codon 29 of the MATR3 protein (p.Leu29Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of distal myopathy (Invitae). It has also been observed to segregate with disease in related individuals. 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: Benign; Align-GVGD: Class C1). 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. 5

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

Last Updated: Nov 27, 2021

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