NM_000362.5(TIMP3):c.271T>C (p.Cys91Arg) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 25, 2020
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:: RCV001301026.7

Allele description

NM_000362.5(TIMP3):c.271T>C (p.Cys91Arg)

Genes:

TIMP3:TIMP metallopeptidase inhibitor 3 [Gene - OMIM - HGNC]
SYN3:synapsin III [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_000362.5(TIMP3):c.271T>C (p.Cys91Arg)

HGVS:

NC_000022.11:g.32857315T>C
NG_009117.2:g.60611T>C
NG_029545.1:g.206076A>G
NG_029545.2:g.206066A>G
NM_000362.5:c.271T>CMANE SELECT
NM_001135774.2:c.708+7600A>G
NM_001369907.1:c.711+7600A>G
NM_001369908.1:c.711+7600A>G
NM_001369909.1:c.708+7600A>G
NM_001369910.1:c.708+7600A>G
NM_003490.4:c.711+7600A>GMANE SELECT
NM_133633.3:c.711+7600A>G
NP_000353.1:p.Cys91Arg
NC_000022.10:g.33253302T>C

Protein change:

C91R

Links:

dbSNP: rs2048398134

NCBI 1000 Genomes Browser:

rs2048398134

Molecular consequence:

NM_001135774.2:c.708+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369907.1:c.711+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369908.1:c.711+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369909.1:c.708+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369910.1:c.708+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_003490.4:c.711+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_133633.3:c.711+7600A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000362.5:c.271T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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maturase K (chloroplast) [Nasa weigendii]
maturase K (chloroplast) [Nasa weigendii]
gi|1447651603|gb|AXM90675.1|

Protein
Homo sapiens myosin binding protein H like (MYBPHL), transcript variant 1, mRNA
Homo sapiens myosin binding protein H like (MYBPHL), transcript variant 1, mRNA
gi|1519244699|ref|NM_001010985.3|

Nucleotide
Human vesicular monoamine transporter VMAT1 mRNA, complete cds
Human vesicular monoamine transporter VMAT1 mRNA, complete cds
gi|1314289|gb|U39905.1|HSU39905

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001490183	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 25, 2020)	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

SCV001490183

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 25, 2020)

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 Invitae, SCV001490183.5

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with TIMP3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces cysteine with arginine at codon 91 of the TIMP3 protein (p.Cys91Arg). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and arginine.

#	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 1, 2024

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