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NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys) AND Welander distal myopathy

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Dec 15, 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:
RCV000576901.16

Allele description [Variation Report for NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys)]

NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys)

Gene:
TIA1:TIA1 cytotoxic granule associated RNA binding protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p13.3
Genomic location:
Preferred name:
NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys)
HGVS:
  • NC_000002.12:g.70212730C>T
  • NG_029967.1:g.40918G>A
  • NM_001351508.2:c.1147G>A
  • NM_001351509.2:c.1123G>A
  • NM_001351510.2:c.1114G>A
  • NM_001351511.1:c.1039G>A
  • NM_001351512.1:c.1012G>A
  • NM_001351513.1:c.1006G>A
  • NM_001351514.2:c.922G>A
  • NM_001351515.2:c.847G>A
  • NM_001351517.2:c.727G>A
  • NM_001351524.2:c.730G>A
  • NM_001351525.2:c.730G>A
  • NM_022037.4:c.1117G>A
  • NM_022173.4:c.1150G>AMANE SELECT
  • NP_001338437.1:p.Glu383Lys
  • NP_001338438.1:p.Glu375Lys
  • NP_001338439.1:p.Glu372Lys
  • NP_001338440.1:p.Glu347Lys
  • NP_001338441.1:p.Glu338Lys
  • NP_001338442.1:p.Glu336Lys
  • NP_001338443.1:p.Glu308Lys
  • NP_001338444.1:p.Glu283Lys
  • NP_001338446.1:p.Glu243Lys
  • NP_001338453.1:p.Glu244Lys
  • NP_001338454.1:p.Glu244Lys
  • NP_071320.2:p.Glu373Lys
  • NP_071505.2:p.Glu384Lys
  • NC_000002.11:g.70439862C>T
  • NM_022173.2:c.1150G>A
  • NR_147216.1:n.1507G>A
  • NR_147217.1:n.1388G>A
  • NR_147218.1:n.1385G>A
  • NR_147219.2:n.1457G>A
  • NR_147220.2:n.1443G>A
  • NR_147221.2:n.1514G>A
  • NR_147222.2:n.1509G>A
  • NR_147223.2:n.1567G>A
  • NR_147224.2:n.1445G>A
  • NR_147225.2:n.1600G>A
  • NR_147226.2:n.1448G>A
  • NR_147227.2:n.1518G>A
  • NR_147228.2:n.1481G>A
  • NR_147229.2:n.1424G>A
  • NR_147230.2:n.1666G>A
  • NR_147231.2:n.1478G>A
  • NR_147232.2:n.1351G>A
  • P31483:p.Glu384Lys
Protein change:
E243K; GLU384LYS
Links:
UniProtKB: P31483#VAR_069897; OMIM: 603518.0001; dbSNP: rs747068278
NCBI 1000 Genomes Browser:
rs747068278
Molecular consequence:
  • NM_001351508.2:c.1147G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351509.2:c.1123G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351510.2:c.1114G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351511.1:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351512.1:c.1012G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351513.1:c.1006G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351514.2:c.922G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351515.2:c.847G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351517.2:c.727G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351524.2:c.730G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351525.2:c.730G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022037.4:c.1117G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022173.4:c.1150G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_147216.1:n.1507G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147217.1:n.1388G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147218.1:n.1385G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147219.2:n.1457G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147220.2:n.1443G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147221.2:n.1514G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147222.2:n.1509G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147223.2:n.1567G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147224.2:n.1445G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147225.2:n.1600G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147226.2:n.1448G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147227.2:n.1518G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147228.2:n.1481G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147229.2:n.1424G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147230.2:n.1666G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147231.2:n.1478G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147232.2:n.1351G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Welander distal myopathy (WDM)
Synonyms:
MUSCULAR DYSTROPHY, DISTAL, LATE-ONSET, AUTOSOMAL DOMINANT; Gower's muscular dystrophy; Welander distal myopathy, Swedish type; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011466; MedGen: C0221054; Orphanet: 603; OMIM: 604454

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000678313OMIM
no assertion criteria provided
Pathogenic
(Apr 1, 2013)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000964805Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 15, 2023)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic linkage of Welander distal myopathy to chromosome 2p13.

Ahlberg G, von Tell D, Borg K, Edström L, Anvret M.

Ann Neurol. 1999 Sep;46(3):399-404.

PubMed [citation]
PMID:
10482271

Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.

Klar J, Sobol M, Melberg A, Mäbert K, Ameur A, Johansson AC, Feuk L, Entesarian M, Orlén H, Casar-Borota O, Dahl N.

Hum Mutat. 2013 Apr;34(4):572-7. doi: 10.1002/humu.22282.

PubMed [citation]
PMID:
23348830
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000678313.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

By targeted high-throughput sequencing and Sanger sequencing of the candidate Welander distal myopathy (WDM; 604454) region on chromosome 2p13, Hackman et al. (2013) identified a heterozygous 1362G-A transition in exon 13 of the TIA1 gene, resulting in a glu384-to-lys (E384K; 603518.0001) substitution that segregated with the disorder in all 57 Swedish and Finnish patients studied. The same mutation was also found in 3 patients from Great Britain who had a partially shared haplotype with the Nordic patients, indicating common ancestry. The mutation was not found in 202 Finnish control samples. The E384K mutation occurred at a highly conserved residue in the RNA-binding domain of the protein at the C terminus, also known as the prion-related domain that is required for TIA1 aggregation in stress granules. Immunofluorescence microscopy of patient muscle showed diffuse TIA1-labeled cytoplasmic aggregates or granules in some atrophic fibers and fibers containing rimmed vacuoles. However, most fibers appeared normal and had normal TIA1 nuclear localization. Analysis of TIA1 splice isoforms and protein stability showed no consistent differences between WDM muscle and control muscle. Expression of the mutant protein in HeLa cells resulted in a mild increased (10-20%) of stress granule numbers compared to controls. The increased number was apparently due to a change in stress-granule dynamics resulting from a gain of function.

Klar et al. (2013) also restricted the WDM-associated haplotype and performed exome sequencing of 43 patients from 35 families with the disorder. They identified a heterozygous E384K mutation resulting from a 1150G-A transition in the TIA1 gene and occurring in a Q-rich domain. The mutation was not found in 800 control chromosomes. Patient muscle biopsies showed increased splicing of exon 7 of the SMN2 gene (601627), reflecting impaired TIA1 function. Klar et al. (2013) hypothesized that reduced activity of TIA1 may result in decreased response to cellular stress, such as oxidative stress, that may cause age-related cellular atrophy in patients carrying the mutation. The age of the mutation was estimated to be 1,050 years earlier, coinciding with the epoch of early seafaring across the Baltic Sea.

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

From Invitae, SCV000964805.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 384 of the TIA1 protein (p.Glu384Lys). This variant is present in population databases (rs747068278, gnomAD 0.007%). This missense change has been observed in individuals with Welander distal myopathy (WDM) (PMID: 10482271, 23348830, 23401021, 27282841). It is commonly reported in individuals of Finnish ancestry (PMID: 10482271, 23348830, 23401021, 27282841). ClinVar contains an entry for this variant (Variation ID: 41480). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Experimental studies have shown that this missense change affects TIA1 function (PMID: 23401021, 28817800). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jun 23, 2024