TTC39C

Chr 18

tetratricopeptide repeat domain 39C

Also known as: C18orf17, HsT2697

NCBI Gene: 125488 ENSG00000168234 UniProt: Q8N584

The TTC39C protein is predicted to be involved in cilium assembly and otolith morphogenesis. Mutations in this gene have not been definitively associated with human disease. The gene shows relatively low constraint against loss-of-function variants, suggesting it may be more tolerant to complete loss of function.

ResearchSummary from RefSeq

Predicted to be involved in cilium assembly and otolith morphogenesis. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.58

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.58LOEUF

pLI 0.000

Z-score 3.47

OE 0.36 (0.23–0.58)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.43Z-score

OE missense 0.77 (0.69–0.85)

226 obs / 295.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.36 (0.23–0.58)

0≤0.351.4

Missense OE?0.77 (0.69–0.85)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 12 / 33.8Missense obs/exp: 226 / 295.1Syn Z: 0.61

Background carrier burden — how many people carry a rare variant somewhere in TTC39C?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 100

688 rare PASS variants

Rare truncating (LoF)

1 in 1,500

102 rare PASS variants

Rare synonymous (reference)

1 in 170

296 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for TTC39C. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 110	1 in 2,000
South Asian	~43k	1 in 87	1 in 970
Remaining (unassigned)	~30k	1 in 100	1 in 3,300
European (Finnish)	~27k	1 in 550	≈ 1 in 5,800
Admixed American	~22k	1 in 120	1 in 3,000
African / African American	~21k	1 in 130	1 in 800
East Asian	~20k	1 in 99	1 in 580
Ashkenazi Jewish	~13k	1 in 390	≈ 1 in 4,400
Middle Eastern	~2,884	1 in 320	1 in 440

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 12 of 14 coding exons well covered in gnomAD exomes; exons 1, 12 marginal. Genomes: all 14.? see exons ↓