TMEM17

transmembrane protein 17

Basic information

Region (hg38): 2:62500218-62511894

Links

ENSG00000186889 ∙ NCBI:200728 ∙ OMIM:614950 ∙ HGNC:26623 ∙ Uniprot:Q86X19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM17 gene.

• not_specified (23 variants)
• Meckel-Gruber_syndrome (1 variants)
• Orofaciodigital_syndrome_I (1 variants)
• Joubert_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM17 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198276.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM17	protein_coding	protein_coding	ENST00000335390	4	11674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00943	0.827	125665	0	5	125670	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.409	93	105	0.887	0.00000520	1289
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000576	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000880
Middle Eastern	0.0000576	0.0000544
South Asian	0.0000702	0.0000653
Other	0.000167	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.257
• hipred: N
• hipred_score: 0.198
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem17

Gene ontology

• Biological process: smoothened signaling pathway;cilium assembly;non-motile cilium assembly
• Cellular component: integral component of membrane;ciliary transition zone;MKS complex;ciliary membrane
• Molecular function: protein binding