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NM_001382567.1(STIM1):c.1213G>A (p.Val405Ile) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 17, 2022
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:
RCV002297098.4

Allele description [Variation Report for NM_001382567.1(STIM1):c.1213G>A (p.Val405Ile)]

NM_001382567.1(STIM1):c.1213G>A (p.Val405Ile)

Gene:
STIM1:stromal interaction molecule 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_001382567.1(STIM1):c.1213G>A (p.Val405Ile)
HGVS:
  • NC_000011.10:g.4082957G>A
  • NG_016277.1:g.232255G>A
  • NM_001277961.3:c.1213G>A
  • NM_001277962.2:c.1213G>A
  • NM_001382566.1:c.991G>A
  • NM_001382567.1:c.1213G>AMANE SELECT
  • NM_001382568.1:c.1213G>A
  • NM_001382569.1:c.1078G>A
  • NM_001382570.1:c.985G>A
  • NM_001382571.1:c.733G>A
  • NM_001382573.1:c.991G>A
  • NM_001382575.1:c.991G>A
  • NM_001382576.1:c.991G>A
  • NM_001382577.1:c.991G>A
  • NM_001382578.1:c.991G>A
  • NM_001382579.1:c.991G>A
  • NM_001382580.1:c.724G>A
  • NM_001382581.1:c.724G>A
  • NM_003156.4:c.1213G>A
  • NP_001264890.1:p.Val405Ile
  • NP_001264891.1:p.Val405Ile
  • NP_001369495.1:p.Val331Ile
  • NP_001369496.1:p.Val405Ile
  • NP_001369497.1:p.Val405Ile
  • NP_001369498.1:p.Val360Ile
  • NP_001369499.1:p.Val329Ile
  • NP_001369500.1:p.Val245Ile
  • NP_001369502.1:p.Val331Ile
  • NP_001369504.1:p.Val331Ile
  • NP_001369505.1:p.Val331Ile
  • NP_001369506.1:p.Val331Ile
  • NP_001369507.1:p.Val331Ile
  • NP_001369508.1:p.Val331Ile
  • NP_001369509.1:p.Val242Ile
  • NP_001369510.1:p.Val242Ile
  • NP_003147.2:p.Val405Ile
  • NP_003147.2:p.Val405Ile
  • LRG_164t1:c.1213G>A
  • LRG_164:g.232255G>A
  • LRG_164p1:p.Val405Ile
  • NC_000011.9:g.4104187G>A
  • NM_003156.3:c.1213G>A
  • NR_168437.1:n.1642G>A
  • NR_168438.1:n.1464G>A
Protein change:
V242I
Molecular consequence:
  • NM_001277961.3:c.1213G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001277962.2:c.1213G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382566.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382567.1:c.1213G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382568.1:c.1213G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382569.1:c.1078G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382570.1:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382571.1:c.733G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382573.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382575.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382576.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382577.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382578.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382579.1:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382580.1:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382581.1:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003156.4:c.1213G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_168437.1:n.1642G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_168438.1:n.1464G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Stormorken syndrome (STRMK)
Synonyms:
THROMBOCYTOPATHY, ASPLENIA, AND MIOSIS
Identifiers:
MONDO: MONDO:0008497; MedGen: C1861451; Orphanet: 3204; OMIM: 185070
Name:
Combined immunodeficiency due to STIM1 deficiency
Synonyms:
Immune dysfunction with T-cell inactivation due to calcium entry defect 2; STIM1 DEFICIENCY; IMMUNODEFICIENCY 10
Identifiers:
MONDO: MONDO:0013008; MedGen: C2748557; Orphanet: 169090; Orphanet: 317430; OMIM: 612783
Name:
Myopathy with tubular aggregates (TAM)
Synonyms:
Tubular Aggregate Myopathy
Identifiers:
MONDO: MONDO:0008051; MedGen: C0410207; OMIM: PS160565

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002597600Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Oct 17, 2022)
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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002597600.3

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

Description

This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 405 of the STIM1 protein (p.Val405Ile). This variant is not present in population databases (gnomAD no frequency). 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. 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 disruptive. This variant has not been reported in the literature in individuals affected with STIM1-related conditions.

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

Last Updated: Sep 29, 2024