NM_000222.3(KIT):c.1781C>T (p.Thr594Ile) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 20, 2023
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:: RCV003237870.11

Allele description [Variation Report for NM_000222.3(KIT):c.1781C>T (p.Thr594Ile)]

NM_000222.3(KIT):c.1781C>T (p.Thr594Ile)

Gene:

KIT:KIT proto-oncogene, receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_000222.3(KIT):c.1781C>T (p.Thr594Ile)

HGVS:

NC_000004.12:g.54727829C>T
NG_007456.1:g.74835C>T
NM_000222.3:c.1781C>TMANE SELECT
NM_001093772.2:c.1769C>T
NM_001385284.1:c.1784C>T
NM_001385285.1:c.1781C>T
NM_001385286.1:c.1769C>T
NM_001385288.1:c.1772C>T
NM_001385290.1:c.1784C>T
NM_001385292.1:c.1772C>T
NP_000213.1:p.Thr594Ile
NP_000213.1:p.Thr594Ile
NP_001087241.1:p.Thr590Ile
NP_001372213.1:p.Thr595Ile
NP_001372214.1:p.Thr594Ile
NP_001372215.1:p.Thr590Ile
NP_001372217.1:p.Thr591Ile
NP_001372219.1:p.Thr595Ile
NP_001372221.1:p.Thr591Ile
LRG_307t1:c.1781C>T
LRG_307:g.74835C>T
LRG_307p1:p.Thr594Ile
NC_000004.11:g.55593995C>T
NM_000222.2:c.1781C>T

Protein change:

T590I

Links:

dbSNP: rs375351432

NCBI 1000 Genomes Browser:

rs375351432

Molecular consequence:

NM_000222.3:c.1781C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001093772.2:c.1769C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385284.1:c.1784C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385285.1:c.1781C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385286.1:c.1769C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385288.1:c.1772C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385290.1:c.1784C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385292.1:c.1772C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002010059	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004025665	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 20, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002010059

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 3, 2021)

germline

clinical testing

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

SCV004025665

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 20, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical 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 Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002010059.3

#	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	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV004025665.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27027238, 32441621)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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