TEKT3

tektin 3, the group of Tektins

Basic information

Region (hg38): 17:15303810-15341632

Links

ENSG00000125409 ∙ NCBI:64518 ∙ OMIM:612683 ∙ HGNC:14293 ∙ Uniprot:Q9BXF9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 81 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 81	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	36708031

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TEKT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEKT3 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			36
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	0	0

Variants in TEKT3

This is a list of pathogenic ClinVar variants found in the TEKT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-15303955-C-T		not specified	Uncertain significance (May 10, 2022)
17-15303961-G-C		not specified	Uncertain significance (Oct 05, 2023)
17-15304004-C-G		not specified	Uncertain significance (Jan 26, 2022)
17-15304004-C-T		not specified	Uncertain significance (Mar 30, 2024)
17-15304042-T-C		not specified	Uncertain significance (Jan 26, 2023)
17-15304121-T-C		not specified	Uncertain significance (Jun 17, 2024)
17-15304141-T-G		not specified	Uncertain significance (Apr 27, 2022)
17-15304142-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-15308671-G-C		not specified	Uncertain significance (Jan 24, 2024)
17-15308700-G-A		not specified	Uncertain significance (Mar 29, 2023)
17-15312296-G-A		not specified	Uncertain significance (Oct 06, 2023)
17-15312308-A-G		not specified	Uncertain significance (Apr 27, 2023)
17-15312369-C-A		not specified	Uncertain significance (Jun 24, 2022)
17-15312431-C-T		not specified	Uncertain significance (Dec 02, 2022)
17-15312435-G-C		not specified	Uncertain significance (Nov 19, 2022)
17-15312447-C-T		not specified	Uncertain significance (Sep 14, 2023)
17-15314094-C-A		not specified	Uncertain significance (May 13, 2024)
17-15314141-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-15314169-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-15314175-C-A		not specified	Uncertain significance (Jan 05, 2022)
17-15314177-G-A		not specified	Uncertain significance (Sep 07, 2022)
17-15314207-T-C		not specified	Uncertain significance (Apr 11, 2023)
17-15314213-T-G		Spermatogenic failure 81	Pathogenic (Mar 07, 2023)
17-15327993-G-A		not specified	Uncertain significance (Sep 16, 2021)
17-15328024-C-A		not specified	Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEKT3	protein_coding	protein_coding	ENST00000395930	7	37831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.98e-17	0.00373	124860	7	881	125748	0.00354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.203	289	299	0.967	0.0000185	3219
Missense in Polyphen		81	88.054	0.91989		1028
Synonymous	0.729	105	115	0.913	0.00000730	949
Loss of Function	-0.207	25	23.9	1.05	0.00000154	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0263	0.0263
Ashkenazi Jewish	0.00	0.00
East Asian	0.00861	0.00622
Finnish	0.00	0.00
European (Non-Finnish)	0.00118	0.00115
Middle Eastern	0.00861	0.00622
South Asian	0.00579	0.00540
Other	0.00197	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a structural component of the sperm flagellum. Required for normal sperm mobility. {ECO:0000250|UniProtKB:Q6X6Z7}.

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.974
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.51

Haploinsufficiency Scores

• pHI: 0.0493
• hipred: N
• hipred_score: 0.306

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0446

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tekt3
• Phenotype: cellular phenotype; reproductive system phenotype

Zebrafish Information Network

• Gene name: tekt3
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: flagellated sperm motility;cilium assembly;cilium movement involved in cell motility;regulation of brood size
• Cellular component: acrosomal membrane;outer acrosomal membrane;nucleus;sperm flagellum;extracellular exosome
• Molecular function: molecular_function;protein binding