TMEM80

protein-coding

transmembrane protein 80

Gene summary

Predicted to be involved in non-motile cilium assembly. Predicted to be located in cilium and membrane. Predicted to be active in ciliary transition zone. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001042463.3

Inheritance

—

ClinVar variants

U:32B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.92

Max pathogenic AF

—

Genomic locus

chr11:695,591-705,028

External References & Databases

Ensembl (ENSG00000177042)

Transcript & Mutation Effects

hg38 • Region Span ~9.4 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 TMEM80 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042463.3. 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			32 clinvar	5 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	7	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042463.3	RefSeq	NP_001035928.3	5	MANE Select
ENST00000397510.9	Ensembl	ENSP00000380646.4	5	MANE Select
NM_001276253.2	RefSeq	NP_001263182.2	4	Standard
NM_001276274.2	RefSeq	NP_001263203.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

non-motile cilium assembly

Cellular Component

integral component of membrane
ciliary transition zone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000608174
Coding exons: 5
Length: 9601
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.442	74	85.5	0.865	0.00000545	1024
Missense (PolyPhen)		25	33.21	0.75279		403
Synonymous	-1.39	57	45.2	1.26	0.00000340	388
Loss of Function	-1.94	10	5.21	1.92	2.21e-7	78

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00038	0.00038	rare
South Asian	0.00020	0.00020	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.271
RVIS EVS: 0.35
RVIS percentile EVS: 74.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00408