TMEM242

protein-coding

transmembrane protein 242

Gene summary

Involved in mitochondrial proton-transporting ATP synthase complex assembly. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf35

MANE transcript

NM_018452.6

Inheritance

—

ClinVar variants

U:26B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr6:157,289,025-157,323,601

External References & Databases

Ensembl (ENSG00000215712)

Transcript & Mutation Effects

hg38 • Region Span ~34.6 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 TMEM242 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018452.6. 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			2 clinvar			2
missense			23 clinvar	1 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	26	1	0	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018452.6	RefSeq	NP_060922.2	4	MANE Select
ENST00000400788.9	Ensembl	ENSP00000383594.3	4	MANE Select
ENST00000367144.4	Ensembl	ENSP00000356112.3	3	Standard
ENST00000367144.5	Ensembl	ENSP00000356112.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400788
Coding exons: 4
Length: 34216
Individuals with no LoFs: 124745
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 124796
p: 0.000204

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.246	75	81.3	0.923	0.00000420	893
Missense (PolyPhen)		21	26.233	0.80052		295
Synonymous	0.153	33	34.1	0.967	0.00000204	293
Loss of Function	0.342	7	8.05	0.870	4.92e-7	79

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000065	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00027	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.112

Intolerance Scores

RVIS EVS: 0.24
RVIS percentile EVS: 68.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
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