NM_001382567.1(STIM1):c.1400A>G (p.Asn467Ser) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 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:: RCV003798069.1

Allele description [Variation Report for NM_001382567.1(STIM1):c.1400A>G (p.Asn467Ser)]

NM_001382567.1(STIM1):c.1400A>G (p.Asn467Ser)

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.1400A>G (p.Asn467Ser)

HGVS:

NC_000011.10:g.4083424A>G
NG_016277.1:g.232722A>G
NM_001277961.3:c.1400A>G
NM_001277962.2:c.1400A>G
NM_001382566.1:c.1178A>G
NM_001382567.1:c.1400A>GMANE SELECT
NM_001382568.1:c.1421A>G
NM_001382569.1:c.1265A>G
NM_001382570.1:c.1172A>G
NM_001382571.1:c.920A>G
NM_001382573.1:c.1178A>G
NM_001382575.1:c.1178A>G
NM_001382576.1:c.1178A>G
NM_001382577.1:c.1178A>G
NM_001382578.1:c.1178A>G
NM_001382579.1:c.1178A>G
NM_001382580.1:c.911A>G
NM_001382581.1:c.911A>G
NM_003156.4:c.1400A>G
NP_001264890.1:p.Asn467Ser
NP_001264891.1:p.Asn467Ser
NP_001369495.1:p.Asn393Ser
NP_001369496.1:p.Asn467Ser
NP_001369497.1:p.Asn474Ser
NP_001369498.1:p.Asn422Ser
NP_001369499.1:p.Asn391Ser
NP_001369500.1:p.Asn307Ser
NP_001369502.1:p.Asn393Ser
NP_001369504.1:p.Asn393Ser
NP_001369505.1:p.Asn393Ser
NP_001369506.1:p.Asn393Ser
NP_001369507.1:p.Asn393Ser
NP_001369508.1:p.Asn393Ser
NP_001369509.1:p.Asn304Ser
NP_001369510.1:p.Asn304Ser
NP_003147.2:p.Asn467Ser
NP_003147.2:p.Asn467Ser
LRG_164t1:c.1400A>G
LRG_164:g.232722A>G
LRG_164p1:p.Asn467Ser
NC_000011.9:g.4104654A>G
NM_003156.3:c.1400A>G
NR_168437.1:n.1829A>G
NR_168438.1:n.1651A>G

Protein change:

N304S

Molecular consequence:

NM_001277961.3:c.1400A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001277962.2:c.1400A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382566.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382567.1:c.1400A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382568.1:c.1421A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382569.1:c.1265A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382570.1:c.1172A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382571.1:c.920A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382573.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382575.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382576.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382577.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382578.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382579.1:c.1178A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382580.1:c.911A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382581.1:c.911A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003156.4:c.1400A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_168437.1:n.1829A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_168438.1:n.1651A>G - 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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txid324869[Organism:noexp] (93)
Identical Protein Groups
BioProject Links for Protein (Select 1060099070) (2)
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Taxonomy Links for Protein (Select 194386310) (1)
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1945343[uid] (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004578793	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 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

SCV004578793

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004578793.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt STIM1 protein function. This variant has not been reported in the literature in individuals affected with STIM1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 467 of the STIM1 protein (p.Asn467Ser).

#	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: Mar 5, 2024

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