TMEM17

protein-coding

transmembrane protein 17

Gene summary

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

MANE transcript

NM_198276.3

Inheritance

—

ClinVar variants

U:32B:2

Top phenotype

Meckel-Gruber syndrome

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr2:62,500,218-62,511,894

External References & Databases

Ensembl (ENSG00000186889)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 TMEM17 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 28

Meckel-Gruber syndromeTotal: 1

not providedTotal: 1

Orofaciodigital syndrome ITotal: 1

Joubert syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198276.3. 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						0
missense			30 clinvar	2 clinvar		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	32	2	0	34

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198276.3	RefSeq	NP_938017.2	4	MANE Select
ENST00000335390.6	Ensembl	ENSP00000335094.5	4	MANE Select
ENST00000944682.1	Ensembl	ENSP00000614741.1	5	Standard
ENST00000944682.2	Ensembl	ENSP00000614741.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

smoothened signaling pathway
cilium assembly
non-motile cilium assembly

Molecular Function

protein binding

Cellular Component

integral component of membrane
ciliary transition zone
MKS complex
ciliary membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335390
Coding exons: 4
Length: 11674
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125670
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.409	93	105	0.887	0.00000520	1289
Missense (PolyPhen)		26	38.404	0.677		502
Synonymous	-1.75	52	38.2	1.36	0.00000183	378
Loss of Function	1.11	4	7.22	0.554	3.03e-7	100

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000058	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000070	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transmembrane component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required for ciliogenesis and sonic hedgehog/SHH signaling (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.336
RVIS EVS: 0.31
RVIS percentile EVS: 72.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.121

Gene Damage Prediction

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