TTC29

protein-coding

tetratricopeptide repeat domain 29, the group of Tetratricopeptide repeat domain containing

Gene summary

Involved in cilium movement and cilium organization. Located in sperm principal piece. Implicated in spermatogenic failure 42. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_031956.4

Inheritance

ClinVar variants

P:11U:72B:5

Top phenotype

Spermatogenic failure 42

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr4:146,706,617-146,945,882

External References & Databases

Ensembl (ENSG00000137473)

Transcript & Mutation Effects

hg38 • Region Span ~239.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spermatogenic failure 42STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032896

Submitter: Labcorp Genetics (formerly Invitae)

non-syndromic male infertility due to sperm motility disorderSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017173

Submitter: Orphanet

Clinical Genomic Database (CGD)

Spermatogenic failure 42AR

Manifestation: Genitourinary

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 31735292; 31735294

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TTC29 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 75

Spermatogenic failure 42Total: 8

not providedTotal: 7

TTC29-related conditionTotal: 2

Male infertility with spermatogenesis disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031956.4. 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				1 clinvar		1
missense			71 clinvar	4 clinvar		75
nonsense	2 clinvar	2 clinvar				4
start loss						0
frameshift	2 clinvar	2 clinvar	1 clinvar			5
splice donor/acceptor (+/-2bp)	2 clinvar	1 clinvar				3
Total	6	5	72	5	0	88

Highest pathogenic variant AF is 0.000371039

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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_031956.4	RefSeq	NP_114162.2	11	MANE Select
ENST00000325106.9	Ensembl	ENSP00000316740.4	11	MANE Select
NM_001300761.4	RefSeq	NP_001287690.1	12	Standard
NM_001317806.3	RefSeq	NP_001304735.1	11	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325106
Coding exons: 11
Length: 239245
Individuals with no LoFs: 124567
Homozygous LoFs: 0
Heterozygous LoFs: 73
Defined: 124640
p: 0.000293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.399	248	231	1.07	0.0000113	3110
Missense (PolyPhen)		42	46.417	0.90484		607
Synonymous	-0.376	89	84.6	1.05	0.00000417	836
Loss of Function	1.54	16	24.2	0.662	0.00000127	327

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.0010	notable
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00029	0.00028	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00040	0.00035	rare
South Asian	0.000066	0.000065	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0792

Intolerance Scores

RVIS EVS: 1.2
RVIS percentile EVS: 92.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.240

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High