M-15498-G-A

Variant names:

• chrM-15498-G-A
• rs207460003
• ENST00000361789.2:c.752G>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 1P and 4B. PP3 BS2

The ENST00000361789.2(MT-CYB):​c.752G>A​(p.Gly251Asp) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G251S) has been classified as Likely benign.

• Frequency: Mitomap GenBank: 𝑓 0.00020 (AC: 15)
• Consequence: MT-CYB ENST00000361789.2 missense
• Scores: Apogee2 Pathogenic 0.63
• Clinical Significance: Uncertain significance criteria provided, single submitter P:1 U:1 DEAF-/-Infantile-histiocytoid-cardiomyopathy
• Conservation: PhyloP100: 3.78
• Publications: 15 publications found

Genes affected

MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

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

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• mitochondrial complex III deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Leber hereditary optic neuropathy

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PP3: Apogee2 supports a deletorius effect, 0.62684804 >= 0.5 .
• BS2: High AC in GnomadMitoHomoplasmic at 16

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361789.2. 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-CYB	ENST00000361789.2	TSL:6	c.752G>A	p.Gly251Asp	missense	Exon 1 of 1	ENSP00000354554.2

Frequencies

Mitomap GenBank AF: 0.00020 AC: 15

Gnomad homoplasmic AF: 0.00028 AC: 16 AN: 56408

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56408

Alfa AF: 0.000445 Hom.: 2

Mitomap

Disease(s): DEAF-/-Infantile-histiocytoid-cardiomyopathy

Status: Reported

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Histiocytoid cardiomyopathy Pathogenic:1

Sep 01, 2000

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Leigh syndrome Uncertain:1

Oct 17, 2019

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The NC_012920.1:m.15498G>A (YP_003024038.1:p.Gly251Asp) variant in MTCYB gene is interpretated to be a Uncertain Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: PM10, PP4, PP6, BS1, BP5

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
Apogee2	Pathogenic	0.63
Hmtvar	Pathogenic	0.69
AlphaMissense	Uncertain	0.45
PhyloP100		3.8

Other links and lift over

dbSNP: rs207460003; hg19: chrM-15499; COSMIC: COSV104420728; COSMIC: COSV104420728;