TEKT2

tektin 2, the group of Tektins

Basic information

Region (hg38): 1:36084093-36088275

Links

ENSG00000092850 ∙ NCBI:27285 ∙ OMIM:608953 ∙ HGNC:11725 ∙ Uniprot:Q9UIF3 ∙ 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 TEKT2 gene.

• Inborn genetic diseases (19 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEKT2 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				3	1	4
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	19	4	5

Variants in TEKT2

This is a list of pathogenic ClinVar variants found in the TEKT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36084643-G-C			Benign (Nov 12, 2018)
1-36084937-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-36084950-G-A		not specified	Likely benign (May 27, 2022)
1-36085042-G-A		not specified	Uncertain significance (May 04, 2022)
1-36085048-C-T		not specified	Uncertain significance (Jul 26, 2022)
1-36085057-C-T			Benign (Feb 25, 2021)
1-36085058-G-C		not specified	Uncertain significance (Nov 13, 2023)
1-36085074-C-G		not specified	Uncertain significance (Aug 28, 2023)
1-36085075-C-G		not specified	Uncertain significance (Sep 29, 2023)
1-36085223-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-36085859-C-G		not specified	Uncertain significance (May 31, 2023)
1-36085918-G-C		not specified	Uncertain significance (Jul 13, 2021)
1-36085921-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-36085930-T-C		not specified	Uncertain significance (Jan 29, 2024)
1-36085993-C-G		not specified	Uncertain significance (May 03, 2023)
1-36086294-A-G			Benign (Nov 12, 2018)
1-36086745-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-36086798-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-36086817-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-36086984-C-T			Likely benign (Sep 01, 2022)
1-36087002-C-G		not specified	Uncertain significance (Jan 18, 2023)
1-36087232-T-C		not specified	Uncertain significance (Mar 03, 2022)
1-36087238-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-36087239-G-A			Likely benign (Feb 01, 2023)
1-36087453-C-T			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEKT2	protein_coding	protein_coding	ENST00000207457	9	4201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.43e-12	0.133	125612	0	136	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.514	268	245	1.09	0.0000174	2799
Missense in Polyphen		83	74.876	1.1085		852
Synonymous	0.254	100	103	0.968	0.00000671	862
Loss of Function	0.632	19	22.2	0.855	0.00000132	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00344	0.00336
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00114	0.00114
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000273	0.000264
Middle Eastern	0.00114	0.00114
South Asian	0.000327	0.000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Structural component of ciliary and flagellar microtubules. Plays a key role in the assembly or attachment of the inner dynein arm to microtubules in sperm flagella and tracheal cilia. Forms filamentous polymers in the walls of ciliary and flagellar microtubules. {ECO:0000250|UniProtKB:Q922G7}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.963
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.74

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.251
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tekt2
• Phenotype: reproductive system phenotype; respiratory system phenotype; cellular phenotype

Gene ontology

• Biological process: flagellated sperm motility;inner dynein arm assembly;cilium assembly;cilium movement involved in cell motility
• Cellular component: nucleus;cytoplasm;microtubule organizing center;microtubule;sperm flagellum