CMC2

protein-coding

C-X9-C motif containing 2, the group of Mitochondrial respiratory chain complex assembly factors

Gene summary

Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf61

MANE transcript

NM_020188.5

Inheritance

—

ClinVar variants

U:10B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr16:80,966,448-81,020,270

External References & Databases

Ensembl (ENSG00000103121)

Transcript & Mutation Effects

hg38 • Region Span ~53.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CMC2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020188.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar	2 clinvar		11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	2	0	12

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020188.5	RefSeq	NP_064573.1	3	MANE Select
ENST00000219400.8	Ensembl	ENSP00000219400.3	3	MANE Select
NM_001351967.2	RefSeq	NP_001338896.1	3	Standard
NM_001351968.2	RefSeq	NP_001338897.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of proteins
Mitochondrial protein import

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000219400
Coding exons: 3
Length: 44178
Individuals with no LoFs: 125686
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125703
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.648	52	40.4	1.29	0.00000205	530
Missense (PolyPhen)		19	14.121	1.3455		215
Synonymous	-0.178	15	14.2	1.06	7.66e-7	126
Loss of Function	0.982	1	2.76	0.362	1.14e-7	43

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in cytochrome c oxidase biogenesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.0933

Intolerance Scores

RVIS EVS: 0.15
RVIS percentile EVS: 64.11

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium