NM_000362.5(TIMP3):c.70T>G (p.Cys24Gly) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 7, 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:: RCV003563746.1

Allele description

NM_000362.5(TIMP3):c.70T>G (p.Cys24Gly)

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.70T>G (p.Cys24Gly)

HGVS:

NC_000022.11:g.32802071T>G
NG_009117.2:g.5367T>G
NG_029545.1:g.261321A>C
NG_029545.2:g.261310A>C
NM_000362.5:c.70T>GMANE SELECT
NM_001135774.2:c.708+62844A>C
NM_001369907.1:c.711+62844A>C
NM_001369908.1:c.711+62844A>C
NM_001369909.1:c.708+62844A>C
NM_001369910.1:c.708+62844A>C
NM_003490.4:c.711+62844A>CMANE SELECT
NM_133633.3:c.711+62844A>C
NP_000353.1:p.Cys24Gly
NC_000022.10:g.33198057T>G

Protein change:

C24G

Molecular consequence:

NM_001135774.2:c.708+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369907.1:c.711+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369908.1:c.711+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369909.1:c.708+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001369910.1:c.708+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_003490.4:c.711+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_133633.3:c.711+62844A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000362.5:c.70T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens 2-oxoglutarate and iron dependent oxygenase domain containing 3 (OG...
Homo sapiens 2-oxoglutarate and iron dependent oxygenase domain containing 3 (OGFOD3), transcript variant 1, mRNA
gi|1519245952|ref|NM_024648.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004312775	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 7, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 28559085, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004312775

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 7, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease.

Stone EM, Andorf JL, Whitmore SS, DeLuca AP, Giacalone JC, Streb LM, Braun TA, Mullins RF, Scheetz TE, Sheffield VC, Tucker BA.

Ophthalmology. 2017 Sep;124(9):1314-1331. doi: 10.1016/j.ophtha.2017.04.008. Epub 2017 May 27.

PubMed [citation]

PMID:: 28559085
PMCID:: PMC5565704

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, SCV004312775.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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. This variant has not been reported in the literature in individuals affected with TIMP3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 24 of the TIMP3 protein (p.Cys24Gly). This variant disrupts the p.Cys24 amino acid residue in TIMP3. Other variant(s) that disrupt this residue have been observed in individuals with TIMP3-related conditions (PMID: 28559085; Invitae), which suggests that this may be a clinically significant amino acid residue. 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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