NM_001382567.1(STIM1):c.1239-10_1239-9del AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 13, 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:: RCV003809579.2

Allele description [Variation Report for NM_001382567.1(STIM1):c.1239-10_1239-9del]

NM_001382567.1(STIM1):c.1239-10_1239-9del

Gene:

STIM1:stromal interaction molecule 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_001382567.1(STIM1):c.1239-10_1239-9del

HGVS:

NC_000011.10:g.4083251CT[1]
NG_016277.1:g.232549CT[1]
NM_001277961.3:c.1239-10_1239-9del
NM_001277962.2:c.1239-10_1239-9del
NM_001382566.1:c.1017-10_1017-9del
NM_001382567.1:c.1239-10_1239-9delMANE SELECT
NM_001382568.1:c.1250_1251del
NM_001382569.1:c.1104-10_1104-9del
NM_001382570.1:c.1011-10_1011-9del
NM_001382571.1:c.759-10_759-9del
NM_001382573.1:c.1017-10_1017-9del
NM_001382575.1:c.1017-10_1017-9del
NM_001382576.1:c.1017-10_1017-9del
NM_001382577.1:c.1017-10_1017-9del
NM_001382578.1:c.1017-10_1017-9del
NM_001382579.1:c.1017-10_1017-9del
NM_001382580.1:c.750-10_750-9del
NM_001382581.1:c.750-10_750-9del
NM_003156.4:c.1239-10_1239-9del
NP_001369497.1:p.Ser417fs
LRG_164:g.232549CT[1]
NC_000011.9:g.4104481CT[1]
NC_000011.9:g.4104481_4104482del

Protein change:

S417fs

Molecular consequence:

NM_001382568.1:c.1250_1251del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001277961.3:c.1239-10_1239-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001277962.2:c.1239-10_1239-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382566.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382567.1:c.1239-10_1239-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382569.1:c.1104-10_1104-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382570.1:c.1011-10_1011-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382571.1:c.759-10_759-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382573.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382575.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382576.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382577.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382578.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382579.1:c.1017-10_1017-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382580.1:c.750-10_750-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382581.1:c.750-10_750-9del - intron variant - [Sequence Ontology: SO:0001627]
NM_003156.4:c.1239-10_1239-9del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV004596255	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jun 13, 2023)	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

SCV004596255

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jun 13, 2023)

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, SCV004596255.1

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

#	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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