NM_000362.5(TIMP3):c.110A>G (p.Asn37Ser) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 6, 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:: RCV001983865.3

Allele description

NM_000362.5(TIMP3):c.110A>G (p.Asn37Ser)

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.110A>G (p.Asn37Ser)

HGVS:

NC_000022.11:g.32802111A>G
NG_009117.2:g.5407A>G
NG_029545.1:g.261281T>C
NG_029545.2:g.261270T>C
NM_000362.5:c.110A>GMANE SELECT
NM_001135774.2:c.708+62804T>C
NM_001369907.1:c.711+62804T>C
NM_001369908.1:c.711+62804T>C
NM_001369909.1:c.708+62804T>C
NM_001369910.1:c.708+62804T>C
NM_003490.4:c.711+62804T>CMANE SELECT
NM_133633.3:c.711+62804T>C
NP_000353.1:p.Asn37Ser
NC_000022.10:g.33198097A>G

Protein change:

N37S

Links:

dbSNP: rs554775591

NCBI 1000 Genomes Browser:

rs554775591

Molecular consequence:

NM_001135774.2:c.708+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369907.1:c.711+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369908.1:c.711+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369909.1:c.708+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369910.1:c.708+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_003490.4:c.711+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_133633.3:c.711+62804T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000362.5:c.110A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens protein phosphatase 1 regulatory inhibitor subunit 14C (PPP1R14C), ...
Homo sapiens protein phosphatase 1 regulatory inhibitor subunit 14C (PPP1R14C), mRNA
gi|1519241903|ref|NM_030949.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002279442	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 6, 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

SCV002279442

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 6, 2023)

germline

clinical testing

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

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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, SCV002279442.3

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

Description

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 37 of the TIMP3 protein (p.Asn37Ser). This variant is present in population databases (rs554775591, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with TIMP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1490697). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.

#	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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