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NM_001382567.1(STIM1):c.1474+17_1474+18delinsGT AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 21, 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:
RCV003074647.3

Allele description [Variation Report for NM_001382567.1(STIM1):c.1474+17_1474+18delinsGT]

NM_001382567.1(STIM1):c.1474+17_1474+18delinsGT

Gene:
STIM1:stromal interaction molecule 1 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_001382567.1(STIM1):c.1474+17_1474+18delinsGT
HGVS:
  • NC_000011.10:g.4083515_4083516delinsGT
  • NG_016277.1:g.232813_232814delinsGT
  • NM_001277961.3:c.1474+17_1474+18delinsGT
  • NM_001277962.2:c.1474+17_1474+18delinsGT
  • NM_001382566.1:c.1252+17_1252+18delinsGT
  • NM_001382567.1:c.1474+17_1474+18delinsGTMANE SELECT
  • NM_001382568.1:c.1495+17_1495+18delinsGT
  • NM_001382569.1:c.1339+17_1339+18delinsGT
  • NM_001382570.1:c.1246+17_1246+18delinsGT
  • NM_001382571.1:c.994+17_994+18delinsGT
  • NM_001382573.1:c.*9_*10delinsGT
  • NM_001382575.1:c.1252+17_1252+18delinsGT
  • NM_001382576.1:c.1252+17_1252+18delinsGT
  • NM_001382577.1:c.1252+17_1252+18delinsGT
  • NM_001382578.1:c.1252+17_1252+18delinsGT
  • NM_001382579.1:c.1252+17_1252+18delinsGT
  • NM_001382580.1:c.985+17_985+18delinsGT
  • NM_001382581.1:c.985+17_985+18delinsGT
  • NM_003156.4:c.1474+17_1474+18delinsGT
  • LRG_164:g.232813_232814delinsGT
  • NC_000011.9:g.4104745_4104746delinsGT
Molecular consequence:
  • NM_001382573.1:c.*9_*10delinsGT - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001277961.3:c.1474+17_1474+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001277962.2:c.1474+17_1474+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382566.1:c.1252+17_1252+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382567.1:c.1474+17_1474+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382568.1:c.1495+17_1495+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382569.1:c.1339+17_1339+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382570.1:c.1246+17_1246+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382571.1:c.994+17_994+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382575.1:c.1252+17_1252+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382576.1:c.1252+17_1252+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382577.1:c.1252+17_1252+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382578.1:c.1252+17_1252+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382579.1:c.1252+17_1252+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382580.1:c.985+17_985+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382581.1:c.985+17_985+18delinsGT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003156.4:c.1474+17_1474+18delinsGT - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003453827Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 21, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

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, SCV003453827.2

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

Description

This sequence change falls in intron 10 of the STIM1 gene. It does not directly change the encoded amino acid sequence of the STIM1 protein. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with STIM1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. 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.

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

Last Updated: Sep 29, 2024