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NM_139276.3(STAT3):c.2147C>T (p.Thr716Met) AND not provided

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Sep 1, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000224259.25

Allele description [Variation Report for NM_139276.3(STAT3):c.2147C>T (p.Thr716Met)]

NM_139276.3(STAT3):c.2147C>T (p.Thr716Met)

Gene:
STAT3:signal transducer and activator of transcription 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.2
Genomic location:
Preferred name:
NM_139276.3(STAT3):c.2147C>T (p.Thr716Met)
HGVS:
  • NC_000017.11:g.42316899G>A
  • NG_007370.1:g.76597C>T
  • NM_001369512.1:c.2147C>T
  • NM_001369513.1:c.2147C>T
  • NM_001369514.1:c.2144C>T
  • NM_001369516.1:c.2144C>T
  • NM_001369517.1:c.2145-48C>T
  • NM_001369518.1:c.2145-48C>T
  • NM_001369519.1:c.2142-48C>T
  • NM_001369520.1:c.2142-48C>T
  • NM_001384984.1:c.2063C>T
  • NM_001384985.1:c.2069C>T
  • NM_001384986.1:c.2157-48C>T
  • NM_001384987.1:c.2126C>T
  • NM_001384988.1:c.2099-48C>T
  • NM_001384989.1:c.2048C>T
  • NM_001384990.1:c.2160-48C>T
  • NM_001384991.1:c.2120C>T
  • NM_001384992.1:c.2087C>T
  • NM_001384993.1:c.2145-10C>T
  • NM_003150.4:c.2144C>T
  • NM_139276.3:c.2147C>TMANE SELECT
  • NM_213662.2:c.2145-48C>T
  • NP_001356441.1:p.Thr716Met
  • NP_001356442.1:p.Thr716Met
  • NP_001356443.1:p.Thr715Met
  • NP_001356445.1:p.Thr715Met
  • NP_001371913.1:p.Thr688Met
  • NP_001371914.1:p.Thr690Met
  • NP_001371916.1:p.Thr709Met
  • NP_001371918.1:p.Thr683Met
  • NP_001371920.1:p.Thr707Met
  • NP_001371921.1:p.Thr696Met
  • NP_003141.2:p.Thr715Met
  • NP_644805.1:p.Thr716Met
  • NP_644805.1:p.Thr716Met
  • LRG_112t1:c.2147C>T
  • LRG_112:g.76597C>T
  • LRG_112p1:p.Thr716Met
  • NC_000017.10:g.40468917G>A
  • NM_139276.2:c.2147C>T
  • P40763:p.Thr716Met
Protein change:
T683M; THR716MET
Links:
UniProtKB: P40763#VAR_071888; OMIM: 102582.0008; dbSNP: rs869312892
NCBI 1000 Genomes Browser:
rs869312892
Molecular consequence:
  • NM_001369517.1:c.2145-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369518.1:c.2145-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369519.1:c.2142-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369520.1:c.2142-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001384986.1:c.2157-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001384988.1:c.2099-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001384990.1:c.2160-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001384993.1:c.2145-10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_213662.2:c.2145-48C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369512.1:c.2147C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369513.1:c.2147C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369514.1:c.2144C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369516.1:c.2144C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384984.1:c.2063C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384985.1:c.2069C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384987.1:c.2126C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384989.1:c.2048C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384991.1:c.2120C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384992.1:c.2087C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003150.4:c.2144C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139276.3:c.2147C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000281134Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 3, 2014) 		germlineclinical testing

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

SCV000566572GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Sep 1, 2021) 		germlineclinical testing

Citation Link,

SCV001246592CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Pathogenic
(Sep 1, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000281134.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.000557not providednot provided

From GeneDx, SCV000566572.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Observed in a patient and their parent with autoimmune enteropathy (Slowik et al., 2014); Published functional studies demonstrate variant results in a gain of function effect (Flanagan SE et al., 2014; Milner JD et al., 2015); Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25359994, 30942636, 25038750, 31770611, 33046446, 28960754, 29330115, 26280891)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001246592.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Oct 20, 2024