NM_016065.4(MRPS16):c.220C>T (p.Arg74Cys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 15, 2022
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:: RCV003824447.2

Allele description [Variation Report for NM_016065.4(MRPS16):c.220C>T (p.Arg74Cys)]

NM_016065.4(MRPS16):c.220C>T (p.Arg74Cys)

Genes:

DNAJC9-AS1:DNAJC9 and MRPS16 antisense RNA 1 [Gene - HGNC]
MRPS16:mitochondrial ribosomal protein S16 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.2

Genomic location:

Preferred name:

NM_016065.4(MRPS16):c.220C>T (p.Arg74Cys)

HGVS:

NC_000010.11:g.73251817G>A
NG_008096.1:g.5877C>T
NM_001410935.1:c.220C>T
NM_016065.4:c.220C>TMANE SELECT
NP_001397864.1:p.Arg74Cys
NP_057149.1:p.Arg74Cys
NC_000010.10:g.75011575G>A

Protein change:

R74C

Molecular consequence:

NM_001410935.1:c.220C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016065.4:c.220C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Aldh1a3 aldehyde dehydrogenase 1 family, member A3 [Rattus norvegicus]
Aldh1a3 aldehyde dehydrogenase 1 family, member A3 [Rattus norvegicus]
Gene ID:266603

Gene
266603[uid] AND (alive[prop]) (1)
Gene
discoidin domain-containing receptor 2 precursor [Homo sapiens]
discoidin domain-containing receptor 2 precursor [Homo sapiens]
gi|62420884|ref|NP_006173.2|

Protein
SI [Dasypus novemcinctus]
SI [Dasypus novemcinctus]
Gene ID:101429055

Gene
Homo sapiens microRNA 144 (MIR144), microRNA
Homo sapiens microRNA 144 (MIR144), microRNA
gi|262205324|ref|NR_029685.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004630414	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 15, 2022)	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

SCV004630414

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 15, 2022)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004630414.1

#	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 arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 74 of the MRPS16 protein (p.Arg74Cys). 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: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C55". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with MRPS16-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.004%).

#	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

ClinVar

Relating variation to medicine