TCTE1

t-complex-associated-testis-expressed 1, the group of Dynein regulatory complex

Basic information

Region (hg38): 6:44278734-44297698

Links

ENSG00000146221 ∙ NCBI:202500 ∙ OMIM:186975 ∙ HGNC:11693 ∙ Uniprot:Q5JU00 ∙ 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 TCTE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCTE1 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			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in TCTE1

This is a list of pathogenic ClinVar variants found in the TCTE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44280254-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-44280300-C-T		not specified	Uncertain significance (Nov 15, 2021)
6-44282115-C-T		not specified	Uncertain significance (Aug 16, 2022)
6-44282139-T-A		not specified	Uncertain significance (Jan 22, 2024)
6-44282144-G-T		not specified	Uncertain significance (May 14, 2024)
6-44282147-A-C		not specified	Uncertain significance (Sep 27, 2022)
6-44282225-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-44282232-G-A		not specified	Uncertain significance (Mar 21, 2024)
6-44282252-G-C		not specified	Uncertain significance (Dec 05, 2022)
6-44282265-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-44282354-G-T		not specified	Uncertain significance (Feb 27, 2024)
6-44282469-C-G		not specified	Uncertain significance (Dec 22, 2023)
6-44282478-C-T		TCTE1-related disorder	Likely benign (Feb 16, 2023)
6-44282486-G-T		not specified	Uncertain significance (Jan 03, 2022)
6-44286038-A-C		not specified	Uncertain significance (Jun 12, 2023)
6-44286053-C-T		not specified	Uncertain significance (Mar 06, 2023)
6-44286139-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-44286158-C-T		not specified	Uncertain significance (Jun 28, 2022)
6-44286187-G-A		not specified	Uncertain significance (Mar 16, 2022)
6-44286190-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-44286257-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-44286257-G-C		not specified	Uncertain significance (Oct 20, 2021)
6-44286263-G-A		TCTE1-related disorder	Likely benign (Dec 28, 2022)
6-44286280-A-T		not specified	Uncertain significance (Feb 28, 2024)
6-44286319-A-G		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCTE1	protein_coding	protein_coding	ENST00000371505	4	18979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.73e-11	0.0756	125590	0	158	125748	0.000628

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.840	278	320	0.868	0.0000203	3247
Missense in Polyphen		94	99.886	0.94107		1046
Synonymous	0.989	126	141	0.894	0.00000935	1069
Loss of Function	0.169	16	16.7	0.955	9.67e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000538	0.000537
Ashkenazi Jewish	0.000327	0.000298
East Asian	0.00114	0.00114
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000583	0.000571
Middle Eastern	0.00114	0.00114
South Asian	0.00159	0.00154
Other	0.00100	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the nexin-dynein regulatory complex (N-DRC) a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. May play a role in the assembly of N-DRC. May be required for sperm motility. {ECO:0000250|UniProtKB:A6H639, ECO:0000250|UniProtKB:A8HMZ4}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.48

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.238
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcte1
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: flagellated sperm motility
• Cellular component: cytoplasm;cytoskeleton;sperm flagellum