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NM_001382567.1(STIM1):c.1239-13C>T AND multiple conditions

Germline classification:
Benign (1 submission)
Last evaluated:
Jan 29, 2024
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:
RCV001509684.7

Allele description [Variation Report for NM_001382567.1(STIM1):c.1239-13C>T]

NM_001382567.1(STIM1):c.1239-13C>T

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.1239-13C>T
HGVS:
  • NC_000011.10:g.4083250C>T
  • NG_016277.1:g.232548C>T
  • NM_001277961.3:c.1239-13C>T
  • NM_001277962.2:c.1239-13C>T
  • NM_001382566.1:c.1017-13C>T
  • NM_001382567.1:c.1239-13C>TMANE SELECT
  • NM_001382568.1:c.1247C>T
  • NM_001382569.1:c.1104-13C>T
  • NM_001382570.1:c.1011-13C>T
  • NM_001382571.1:c.759-13C>T
  • NM_001382573.1:c.1017-13C>T
  • NM_001382575.1:c.1017-13C>T
  • NM_001382576.1:c.1017-13C>T
  • NM_001382577.1:c.1017-13C>T
  • NM_001382578.1:c.1017-13C>T
  • NM_001382579.1:c.1017-13C>T
  • NM_001382580.1:c.750-13C>T
  • NM_001382581.1:c.750-13C>T
  • NM_003156.4:c.1239-13C>T
  • NP_001369497.1:p.Ser416Phe
  • LRG_164t1:c.1239-13C>T
  • LRG_164:g.232548C>T
  • NC_000011.9:g.4104480C>T
  • NM_003156.3:c.1239-13C>T
Protein change:
S416F
Links:
dbSNP: rs115353673
NCBI 1000 Genomes Browser:
rs115353673
Molecular consequence:
  • NM_001277961.3:c.1239-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001277962.2:c.1239-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382566.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382567.1:c.1239-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382569.1:c.1104-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382570.1:c.1011-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382571.1:c.759-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382573.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382575.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382576.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382577.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382578.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382579.1:c.1017-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382580.1:c.750-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382581.1:c.750-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003156.4:c.1239-13C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382568.1:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001716522Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Benign
(Jan 29, 2024) 		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, SCV001716522.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024