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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002597600	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 17, 2022)	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

SCV002597600

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 17, 2022)

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, SCV002597600.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	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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