M-6261-G-A

Variant names:

• chrM-6261-G-A
• rs201262114
• ENST00000361624.2:c.358G>A

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4 BP6_Very_Strong BS1 BS2

The ENST00000361624.2(MT-CO1):​c.358G>A​(p.Ala120Thr) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Mitomap GenBank: 𝑓 0.0081 (AC: 496)
• Consequence: MT-CO1 ENST00000361624.2 missense
• Scores: Apogee2 Benign 0.093
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4 Prostate-Cancer-/-LHON
• Conservation: PhyloP100: 7.69
• Publications: 15 publications found

Genes affected

MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]

MT-CO1 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• hereditary recurrent myoglobinuria

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• cytochrome-c oxidase deficiency disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• MELAS syndrome

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet
• mitochondrial non-syndromic sensorineural hearing loss

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet
• Leigh syndrome

  Inheritance: Mitochondrial Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Apogee2 supports a benign effect, 0.09348247 < 0.5 .
• BP6: Variant M-6261-G-A is Benign according to our data. Variant chrM-6261-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 235718.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: High frequency in mitomap database: 0.0081
• BS2: High AC in GnomadMitoHomoplasmic at 401

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361624.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-CO1	ENST00000361624.2	TSL:6	c.358G>A	p.Ala120Thr	missense	Exon 1 of 1	ENSP00000354499.2

Frequencies

Mitomap GenBank AF: 0.0081 AC: 496

Gnomad homoplasmic AF: 0.0071 AC: 401 AN: 56365

Gnomad heteroplasmic AF: 0.00018 AC: 10 AN: 56365

Alfa AF: 0.00971 Hom.: 289

Mitomap

Disease(s): Prostate-Cancer-/-LHON

Status: Reported

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Apr 16, 2019

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jun 15, 2015

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not specified Benign:1

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Leigh syndrome Benign:1

Oct 17, 2019

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The NC_012920.1:m.6261G>A (YP_003024028.1:p.Ala120Thr) variant in MTCO1 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.093
Hmtvar	Pathogenic	0.66
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.43	T
DEOGEN2	Benign	0.0058	T
LIST_S2	Benign	0.71	T
MutationAssessor	Benign	0.47	N
PhyloP100		7.7
PROVEAN	Benign	0.27	N
Sift4G	Benign	0.12	T
GERP RS		4.5
Varity_R		0.31
Mutation Taster		=39/61	disease causing

Other links and lift over

dbSNP: rs201262114; hg19: chrM-6262;