TTC21A

tetratricopeptide repeat domain 21A, the group of MicroRNA protein coding host genes|IFT-A complex|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 3:39107679-39138903

Links

ENSG00000168026 ∙ NCBI:199223 ∙ OMIM:611430 ∙ HGNC:30761 ∙ Uniprot:Q8NDW8 ∙ 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 37 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 37	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	30929735

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TTC21A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC21A 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				2	7	9
missense			67	5	15	87
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	1	67	7	22

Variants in TTC21A

This is a list of pathogenic ClinVar variants found in the TTC21A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-39109095-T-C		TTC21A-related disorder	Likely benign (Nov 14, 2019)
3-39109107-A-G			Uncertain significance (-)
3-39109145-G-T		TTC21A-related disorder	Benign (Nov 25, 2019)
3-39109162-C-G		not specified	Uncertain significance (Mar 21, 2024)
3-39109175-G-A		not specified	Uncertain significance (Dec 16, 2022)
3-39109183-G-C		not specified	Uncertain significance (May 03, 2023)
3-39110062-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-39110854-G-A		TTC21A-related disorder	Benign (Oct 30, 2019)
3-39110913-A-T		not specified	Uncertain significance (Aug 12, 2021)
3-39110923-A-G		Spermatogenic failure 37	Pathogenic (May 13, 2019)
3-39110967-G-A		not specified	Uncertain significance (Jan 30, 2024)
3-39110977-A-G			Uncertain significance (Jun 01, 2024)
3-39110985-C-A		not specified	Uncertain significance (Dec 21, 2022)
3-39110988-A-G		not specified	Uncertain significance (Aug 01, 2022)
3-39112462-A-G		not specified	Uncertain significance (Dec 21, 2023)
3-39112464-G-A		not specified	Uncertain significance (Mar 30, 2024)
3-39112465-T-G		not specified	Uncertain significance (May 28, 2024)
3-39112497-A-G		not specified	Uncertain significance (Aug 12, 2021)
3-39112512-A-G		not specified	Uncertain significance (Apr 20, 2024)
3-39112524-G-A		not specified	Likely benign (Jan 09, 2024)
3-39114630-G-A		not specified	Uncertain significance (Jun 10, 2022)
3-39114645-A-G		not specified	Uncertain significance (Dec 11, 2023)
3-39114743-G-A		Spermatogenic failure 37	Pathogenic (May 14, 2019)
3-39118118-G-A		not specified	Uncertain significance (Feb 05, 2024)
3-39118124-G-A		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC21A	protein_coding	protein_coding	ENST00000431162	29	31243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.89e-24	0.728	124547	0	263	124810	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.949	647	719	0.900	0.0000386	8690
Missense in Polyphen		173	202.53	0.85418		2497
Synonymous	0.164	289	293	0.988	0.0000167	2470
Loss of Function	2.35	48	69.1	0.694	0.00000330	869

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00267	0.00267
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000668	0.000668
Finnish	0.000371	0.000371
European (Non-Finnish)	0.00144	0.00140
Middle Eastern	0.000668	0.000668
South Asian	0.000490	0.000490
Other	0.00132	0.00132

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0985

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.95

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.229
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.405

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc21a

Gene ontology

• Biological process: intraciliary retrograde transport;protein localization to cilium
• Cellular component: cilium;intraciliary transport particle A