TMEM69

protein-coding

transmembrane protein 69

Gene summary

Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C1orf154

MANE transcript

NM_016486.4

Inheritance

—

ClinVar variants

U:29B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr1:45,688,181-45,694,436

External References & Databases

Ensembl (ENSG00000159596)

Transcript & Mutation Effects

hg38 • Region Span ~6.3 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 TMEM69 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 29

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016486.4. 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			28 clinvar	2 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	29	2	0	31

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016486.4	RefSeq	NP_057570.2	2	MANE Select
ENST00000372025.5	Ensembl	ENSP00000361095.4	2	MANE Select
ENST00000871190.1	Ensembl	ENSP00000541249.1	2	Standard
ENST00000871191.1	Ensembl	ENSP00000541250.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372025
Coding exons: 2
Length: 7230
Individuals with no LoFs: 124693
Homozygous LoFs: 0
Heterozygous LoFs: 101
Defined: 124794
p: 0.000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.203	120	126	0.949	0.00000561	1600
Missense (PolyPhen)		24	33.925	0.70744		455
Synonymous	1.40	32	43.8	0.731	0.00000187	510
Loss of Function	0.342	6	6.97	0.860	2.93e-7	93

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00058	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.0037	0.0037	notable
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.00082	0.00082	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.525
RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.474

Gene Damage Prediction

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