rs267606884

Variant names:

• chrM-7275-T-C
• rs267606884
• unassigned_transcript_4799:c.1372T>C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Mitomap GenBank: Absent
• Consequence: COX1 missense
• Scores: Apogee2 Pathogenic 0.68
• Clinical Significance: Pathogenic no assertion criteria provided P:1 No linked disesase in Mitomap
• Conservation: PhyloP100: 7.73

Genes affected

COX1 (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]

TRND (HGNC:7478): (mitochondrially encoded tRNA aspartic acid)

TRNS1 (HGNC:7497): (mitochondrially encoded tRNA serine 1 (UCN))

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: No frequency data in Mitomap. Probably very rare.
• PP5: Variant M-7275-T-C is Pathogenic according to our data. Variant chrM-7275-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 9673.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COX1	unassigned_transcript_4799	c.1372T>C	p.Ser458Pro	missense_variant	Exon 1 of 1
TRND	unassigned_transcript_4801	c.-243T>C		upstream_gene_variant
TRNS1	unassigned_transcript_4800	c.*171A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD4 exome Cov.: 0

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap

No disease associated.

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Familial colorectal cancer Pathogenic:1

Mar 03, 2009

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Apogee2	Pathogenic	0.68
Hmtvar	Pathogenic	0.86
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.055	T
DEOGEN2	Benign	0.18	T
LIST_S2	Uncertain	0.95	D
MutationAssessor	Pathogenic	4.7	H
PROVEAN	Benign	-1.7	N
Sift4G	Uncertain	0.0030	D
GERP RS		5.2
Varity_R		0.96

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs267606884; hg19: chrM-7276;