NM_000362.5(TIMP3):c.322G>A (p.Val108Ile) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 4, 2023
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:: RCV003041413.2

Allele description

NM_000362.5(TIMP3):c.322G>A (p.Val108Ile)

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.322G>A (p.Val108Ile)

HGVS:

NC_000022.11:g.32858022G>A
NG_009117.2:g.61318G>A
NG_029545.1:g.205369C>T
NG_029545.2:g.205359C>T
NM_000362.5:c.322G>AMANE SELECT
NM_001135774.2:c.708+6893C>T
NM_001369907.1:c.711+6893C>T
NM_001369908.1:c.711+6893C>T
NM_001369909.1:c.708+6893C>T
NM_001369910.1:c.708+6893C>T
NM_003490.4:c.711+6893C>TMANE SELECT
NM_133633.3:c.711+6893C>T
NP_000353.1:p.Val108Ile
NC_000022.10:g.33254009G>A

Protein change:

V108I

Molecular consequence:

NM_001135774.2:c.708+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001369907.1:c.711+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001369908.1:c.711+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001369909.1:c.708+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001369910.1:c.708+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_003490.4:c.711+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_133633.3:c.711+6893C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000362.5:c.322G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Xaa-Pro peptidase family protein [Mediterraneibacter sp. 210702-DFI.3.120]
Xaa-Pro peptidase family protein [Mediterraneibacter sp. 210702-DFI.3.120]
gi|2124948735|ref|WP_227155794.1|

Protein
Model organism or animal sample from Ablepharus sikimmensis
Model organism or animal sample from Ablepharus sikimmensis

biosample
Model organism or animal sample from Sphenomorphus jobiensis
Model organism or animal sample from Sphenomorphus jobiensis

biosample
Model organism or animal sample from Tropidophorus cocincinensis
Model organism or animal sample from Tropidophorus cocincinensis

biosample
Whole Genome Sequencing of Amazon molly
Whole Genome Sequencing of Amazon molly

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003444482	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 4, 2023)	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

SCV003444482

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 4, 2023)

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, SCV003444482.2

#	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 output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 2138441). This variant has not been reported in the literature in individuals affected with TIMP3-related conditions. This variant is present in population databases (rs779017473, gnomAD 0.006%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 108 of the TIMP3 protein (p.Val108Ile).

#	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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