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NM_004994.3(MMP9):c.1764G>A (p.Trp588Ter) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 24, 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:
RCV001869136.4

Allele description [Variation Report for NM_004994.3(MMP9):c.1764G>A (p.Trp588Ter)]

NM_004994.3(MMP9):c.1764G>A (p.Trp588Ter)

Genes:
SLC12A5-AS1:SLC12A5 and MMP9 antisense RNA 1 [Gene - HGNC]
MMP9:matrix metallopeptidase 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.12
Genomic location:
Preferred name:
NM_004994.3(MMP9):c.1764G>A (p.Trp588Ter)
HGVS:
  • NC_000020.11:g.46014137G>A
  • NG_011468.1:g.10230G>A
  • NM_004994.3:c.1764G>AMANE SELECT
  • NP_004985.2:p.Trp588Ter
  • NC_000020.10:g.44642776G>A
  • NM_004994.2:c.1764G>A
  • NR_147699.1:n.1320C>T
Protein change:
W588*; TRP588TER
Links:
OMIM: 120361.0002; dbSNP: rs200746714
NCBI 1000 Genomes Browser:
rs200746714
Molecular consequence:
  • NR_147699.1:n.1320C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_004994.3:c.1764G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002316523Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 24, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002316523.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 631876). This variant has not been reported in the literature in individuals affected with MMP9-related conditions. This variant is present in population databases (rs200746714, gnomAD 0.03%). This sequence change creates a premature translational stop signal (p.Trp588*) in the MMP9 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in MMP9 cause disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024