TTC29

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

Basic information

Region (hg38): 4:146706616-146945882

Links

ENSG00000137473 ∙ NCBI:83894 ∙ OMIM:618735 ∙ HGNC:29936 ∙ Uniprot:Q8NA56 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
• spermatogenic failure 42 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 42	AR	General	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	Genitourinary	31735292; 31735294

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TTC29 gene.

• Inborn genetic diseases (12 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC29 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14	1		15
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding				1		1
Total	1	1	14	2	0

Highest pathogenic variant AF is 0.000868

Variants in TTC29

This is a list of pathogenic ClinVar variants found in the TTC29 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-146706824-C-T		Spermatogenic failure 42	Pathogenic (Jan 23, 2020)
4-146707186-A-G		not specified	Uncertain significance (Jul 12, 2022)
4-146707504-G-A		not specified	Uncertain significance (Jul 25, 2023)
4-146803559-G-T		not specified	Uncertain significance (Jul 06, 2021)
4-146803565-T-C		not specified	Uncertain significance (Jan 19, 2024)
4-146803630-T-G		not specified	Uncertain significance (Jun 22, 2023)
4-146803680-G-C		Spermatogenic failure 42	Pathogenic (Jan 24, 2020)
4-146820195-G-A		not specified	Uncertain significance (Oct 27, 2021)
4-146820225-A-T		not specified	Uncertain significance (May 09, 2023)
4-146820234-G-C		not specified	Uncertain significance (Dec 21, 2022)
4-146820239-C-G		not specified	Uncertain significance (Oct 13, 2023)
4-146833805-C-A		Spermatogenic failure 42	Pathogenic (Jan 23, 2020)
4-146833843-C-T			Uncertain significance (Oct 01, 2021)
4-146867532-T-C		not specified	Conflicting classifications of pathogenicity (Dec 16, 2023)
4-146874721-T-C			Uncertain significance (Dec 01, 2021)
4-146874761-G-A			Likely pathogenic (Feb 01, 2022)
4-146874765-G-T		Spermatogenic failure 42	Pathogenic (Jan 23, 2020)
4-146874871-C-T		not specified	Uncertain significance (Apr 20, 2023)
4-146903579-G-A		not specified	Uncertain significance (Jun 16, 2022)
4-146903642-T-C		not specified	Uncertain significance (Dec 08, 2023)
4-146903704-GTTATTATGTACATC-G		Spermatogenic failure 42	Pathogenic (Jan 23, 2020)
4-146909073-T-A		not specified	Uncertain significance (Mar 07, 2024)
4-146909074-C-A		not specified	Uncertain significance (Aug 04, 2023)
4-146909091-TCCTCC-T		Spermatogenic failure 42	Pathogenic (Jan 23, 2020)
4-146909170-C-G		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC29	protein_coding	protein_coding	ENST00000325106	11	239245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-8	0.815	124567	0	73	124640	0.000293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.399	248	231	1.07	0.0000113	3110
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.000105	0.0000994
East Asian	0.000288	0.000278
Finnish	0.0000478	0.0000464
European (Non-Finnish)	0.000399	0.000354
Middle Eastern	0.000288	0.000278
South Asian	0.0000656	0.0000654
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0792

Intolerance Scores

• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.95

Haploinsufficiency Scores

• pHI: 0.0570
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.240

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc29