NM_018127.7(ELAC2):c.1532C>A (p.Ser511Tyr) AND Combined oxidative phosphorylation defect type 17

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 9, 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:: RCV001862661.5

Allele description [Variation Report for NM_018127.7(ELAC2):c.1532C>A (p.Ser511Tyr)]

NM_018127.7(ELAC2):c.1532C>A (p.Ser511Tyr)

Gene:

ELAC2:elaC ribonuclease Z 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p12

Genomic location:

Preferred name:

NM_018127.7(ELAC2):c.1532C>A (p.Ser511Tyr)

HGVS:

NC_000017.11:g.12996674G>T
NG_015808.1:g.26391C>A
NM_001165962.2:c.1412C>A
NM_018127.7:c.1532C>AMANE SELECT
NM_173717.2:c.1529C>A
NP_001159434.1:p.Ser471Tyr
NP_060597.4:p.Ser511Tyr
NP_776065.1:p.Ser510Tyr
NC_000017.10:g.12899991G>T
NC_000017.10:g.12899991G>T
NM_018127.6:c.1532C>A

Protein change:

S471Y

Links:

dbSNP: rs1240684251

NCBI 1000 Genomes Browser:

rs1240684251

Molecular consequence:

NM_001165962.2:c.1412C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_018127.7:c.1532C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_173717.2:c.1529C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Combined oxidative phosphorylation defect type 17
Synonyms:: Combined oxidative phosphorylation deficiency 17
Identifiers:: MONDO: MONDO:0014190; MedGen: C3809526; Orphanet: 369913; OMIM: 615440

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002162738	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 9, 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

SCV002162738

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 9, 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002162738.4

#	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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 870074). This missense change has been observed in individual(s) with clinical features of combined oxidative phosphorylation deficiency (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces serine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 511 of the ELAC2 protein (p.Ser511Tyr).

#	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: Apr 6, 2024

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