TEKT1

tektin 1, the group of Tektins

Basic information

Region (hg38): 17:6789133-6831761

Links

ENSG00000167858 ∙ NCBI:83659 ∙ OMIM:609002 ∙ HGNC:15534 ∙ Uniprot:Q969V4 ∙ 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 TEKT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEKT1 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	29	3	0

Variants in TEKT1

This is a list of pathogenic ClinVar variants found in the TEKT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6800035-C-G		not specified	Uncertain significance (Dec 14, 2023)
17-6800082-T-A		not specified	Uncertain significance (Nov 29, 2021)
17-6800085-C-T		not specified	Uncertain significance (Nov 17, 2023)
17-6800086-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-6800110-G-T		not specified	Uncertain significance (Dec 02, 2022)
17-6800762-G-A		not specified	Uncertain significance (Apr 10, 2023)
17-6800799-C-T		not specified	Uncertain significance (Aug 10, 2021)
17-6800808-G-A		not specified	Uncertain significance (Oct 17, 2023)
17-6800813-A-C		not specified	Uncertain significance (Dec 18, 2023)
17-6800820-C-A		not specified	Uncertain significance (Dec 14, 2022)
17-6800829-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-6800854-A-T		not specified	Uncertain significance (Sep 22, 2023)
17-6800863-C-A		TEKT1-related disorder	Likely benign (Mar 31, 2022)
17-6800919-C-T		not specified	Uncertain significance (Oct 16, 2023)
17-6800933-T-C		not specified	Uncertain significance (Jun 16, 2024)
17-6812865-T-C		TEKT1-related disorder	Likely benign (Aug 02, 2022)
17-6812880-A-G		not specified	Uncertain significance (Jan 19, 2022)
17-6812922-C-T		not specified	Uncertain significance (Apr 15, 2024)
17-6812952-C-T		not specified	Uncertain significance (Mar 15, 2024)
17-6815182-C-T		not specified	Uncertain significance (Apr 23, 2024)
17-6815235-T-C		not specified	Uncertain significance (Apr 28, 2022)
17-6815262-T-A		not specified	Uncertain significance (Apr 04, 2023)
17-6815835-G-A		not specified	Uncertain significance (May 17, 2023)
17-6815844-C-T		not specified	Uncertain significance (May 18, 2023)
17-6815886-C-T		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEKT1	protein_coding	protein_coding	ENST00000338694	7	42629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.95e-7	0.770	125502	0	245	125747	0.000975

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.132	235	241	0.976	0.0000136	2745
Missense in Polyphen		77	78.089	0.98605		865
Synonymous	0.247	94	97.1	0.968	0.00000563	792
Loss of Function	1.30	12	17.9	0.669	9.06e-7	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00166	0.00166
Ashkenazi Jewish	0.00	0.00
East Asian	0.000654	0.000653
Finnish	0.000281	0.000277
European (Non-Finnish)	0.00143	0.00142
Middle Eastern	0.000654	0.000653
South Asian	0.000230	0.000229
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Structural component of ciliary and flagellar microtubules. Forms filamentous polymers in the walls of ciliary and flagellar microtubules.

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.39

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.353

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.198

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tekt1

Zebrafish Information Network

• Gene name: tekt1
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: flagellated sperm motility;cilium assembly;cilium movement involved in cell motility
• Cellular component: nucleus;cytoplasm;microtubule;sperm flagellum
• Molecular function: protein binding