NM_078470.6(COX15):c.*1242A>G AND Leigh syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 13, 2018
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:: RCV001105517.4

Allele description [Variation Report for NM_078470.6(COX15):c.*1242A>G]

NM_078470.6(COX15):c.*1242A>G

Gene:

COX15:cytochrome c oxidase assembly homolog COX15 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_078470.6(COX15):c.*1242A>G

HGVS:

NC_000010.11:g.99713345T>C
NG_008986.1:g.24322A>G
NM_001320974.2:c.1101+3003A>G
NM_001320975.2:c.*1423A>G
NM_001320976.2:c.*1242A>G
NM_001372024.1:c.*461A>G
NM_001372025.1:c.*1242A>G
NM_001372026.1:c.*1242A>G
NM_001372027.1:c.*1346A>G
NM_001372028.1:c.*669A>G
NM_004376.7:c.*69A>G
NM_078470.6:c.*1242A>GMANE SELECT
LRG_406t2:c.*69A>G
LRG_406:g.24322A>G
NC_000010.10:g.101473102T>C
NM_004376.5:c.*69A>G
NR_164009.1:n.2315A>G

Links:

dbSNP: rs2036459883

NCBI 1000 Genomes Browser:

rs2036459883

Molecular consequence:

NM_001320975.2:c.*1423A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001320976.2:c.*1242A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001372024.1:c.*461A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001372025.1:c.*1242A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001372026.1:c.*1242A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001372027.1:c.*1346A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001372028.1:c.*669A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_004376.7:c.*69A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_078470.6:c.*1242A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001320974.2:c.1101+3003A>G - intron variant - [Sequence Ontology: SO:0001627]
NR_164009.1:n.2315A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Leigh syndrome (NULS)
Synonyms:: Leigh Disease; Subacute necrotizing encephalopathy; Necrotizing encephalopathy infantile subacute of Leigh; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009723; MedGen: C0023264; Orphanet: 506; OMIM: 256000

Recent activity

Clear Turn Off Turn On

Mus musculus Smith-Magenis syndrome chromosome region, candidate 8 homolog (huma...
Mus musculus Smith-Magenis syndrome chromosome region, candidate 8 homolog (human) (Smcr8), transcript variant 2, mRNA
gi|146198630|ref|NM_175491.4|

Nucleotide
Homo sapiens v-mos Moloney murine sarcoma viral oncogene homolog, mRNA (cDNA clo...
Homo sapiens v-mos Moloney murine sarcoma viral oncogene homolog, mRNA (cDNA clone MGC:119962 IMAGE:40016104), complete cds
gi|76827707|gb|BC106737.1|

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
SCV001262488	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Jan 13, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001262488

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Jan 13, 2018)

germline

clinical testing

Citation Link

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001262488.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

#	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: May 19, 2024

ClinVar

Relating variation to medicine