NM_007289.4(MME):c.1445A>C (p.Tyr482Ser) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 31, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001767178.6

Allele description [Variation Report for NM_007289.4(MME):c.1445A>C (p.Tyr482Ser)]

NM_007289.4(MME):c.1445A>C (p.Tyr482Ser)

Gene:

MME:membrane metalloendopeptidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q25.2

Genomic location:

Preferred name:

NM_007289.4(MME):c.1445A>C (p.Tyr482Ser)

HGVS:

NC_000003.12:g.155147172A>C
NG_051105.1:g.128049A>C
NM_000902.5:c.1445A>C
NM_001354642.2:c.1445A>C
NM_001354643.1:c.1445A>C
NM_007287.4:c.1445A>C
NM_007288.3:c.1445A>C
NM_007289.4:c.1445A>CMANE SELECT
NP_000893.2:p.Tyr482Ser
NP_001341571.1:p.Tyr482Ser
NP_001341572.1:p.Tyr482Ser
NP_009218.2:p.Tyr482Ser
NP_009219.2:p.Tyr482Ser
NP_009220.2:p.Tyr482Ser
NC_000003.11:g.154864961A>C
NM_007289.2:c.1445A>C

Protein change:

Y482S

Links:

dbSNP: rs201936237

NCBI 1000 Genomes Browser:

rs201936237

Molecular consequence:

NM_000902.5:c.1445A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354642.2:c.1445A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354643.1:c.1445A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_007287.4:c.1445A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_007288.3:c.1445A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_007289.4:c.1445A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001991058	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 11, 2019)	germline	clinical testing	Citation Link,
SCV002188907	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 31, 2021)	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

SCV001991058

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jun 11, 2019)

germline

clinical testing

Citation Link,

SCV002188907

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 31, 2021)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 GeneDx, SCV001991058.2

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002188907.3

#	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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with MME-related conditions. This variant is present in population databases (rs201936237, ExAC 0.002%). This sequence change replaces tyrosine with serine at codon 482 of the MME protein (p.Tyr482Ser). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and serine.

#	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 29, 2024

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