TECTA

tectorin alpha

Basic information

Region (hg38): 11:121101242-121191490

Previous symbols: [ "DFNA12", "DFNA8", "DFNB21" ]

Links

ENSG00000109927 ∙ NCBI:7007 ∙ OMIM:602574 ∙ HGNC:11720 ∙ Uniprot:O75443 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 21 (Strong), mode of inheritance: AD
• autosomal dominant nonsyndromic hearing loss 12 (Strong), mode of inheritance: AR
• autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal dominant nonsyndromic hearing loss 12 (Strong), mode of inheritance: AD
• autosomal recessive nonsyndromic hearing loss 21 (Strong), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 21; Deafness, autosomal dominant 12	AD/AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	9150164; 9718342; 9763681; 10987647; 9590290; 9949200; 11333869; 12746400; 17661817; 17431902; 23226338

ClinVar

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

• not provided (634 variants)
• not specified (197 variants)
• Autosomal dominant nonsyndromic hearing loss 12 (180 variants)
• Autosomal recessive nonsyndromic hearing loss 21 (162 variants)
• Inborn genetic diseases (87 variants)
• Hearing impairment (15 variants)
• TECTA-related condition (15 variants)
• Nonsyndromic genetic hearing loss (11 variants)
• Autosomal dominant nonsyndromic hearing loss 12;Autosomal recessive nonsyndromic hearing loss 21 (11 variants)
• Rare genetic deafness (11 variants)
• Nonsyndromic Hearing Loss, Dominant (5 variants)
• Nonsyndromic Hearing Loss, Recessive (5 variants)
• Meniere disease (5 variants)
• Sensorineural hearing loss disorder (2 variants)
• Bilateral sensorineural hearing impairment (1 variants)
• Congenital sensorineural hearing impairment (1 variants)
• - (1 variants)
• Ear malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TECTA 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			35	113	8	156
missense	2	10	400	23	3	438
nonsense	12	7	2			21
start loss						0
frameshift	11	8				19
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1	5				6
splice region	1	1	9	11		22
non coding			4	51	62	117
Total	26	30	443	187	73

Highest pathogenic variant AF is 0.000105

Variants in TECTA

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

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

Position	Type	Phenotype	Significance	ClinVar
11-121102355-A-C			Benign (Dec 23, 2018)
11-121102565-C-T			Likely benign (Jan 25, 2019)
11-121102587-A-C			Benign (Jul 05, 2018)
11-121102653-T-C		not specified • Nonsyndromic Hearing Loss, Dominant • Nonsyndromic Hearing Loss, Recessive	Benign/Likely benign (Jun 25, 2020)
11-121102676-C-CA		Nonsyndromic genetic hearing loss	Likely pathogenic (Feb 02, 2023)
11-121102688-GA-G		TECTA-related disorder	Likely pathogenic (Jul 19, 2023)
11-121102694-G-C		Autosomal dominant nonsyndromic hearing loss 12	Likely benign (-)
11-121102698-C-A		not specified • Autosomal recessive nonsyndromic hearing loss 21 • Autosomal dominant nonsyndromic hearing loss 12 • TECTA-related disorder	Conflicting classifications of pathogenicity (Apr 28, 2023)
11-121102701-T-G		Autosomal recessive nonsyndromic hearing loss 21	Uncertain significance (Aug 25, 2022)
11-121102710-C-T			Conflicting classifications of pathogenicity (Nov 05, 2021)
11-121102712-C-T			Uncertain significance (Jan 21, 2020)
11-121102721-A-G		not specified • Autosomal dominant nonsyndromic hearing loss 12 • Autosomal recessive nonsyndromic hearing loss 21	Benign/Likely benign (Jan 25, 2024)
11-121102755-C-T			Likely benign (Nov 20, 2020)
11-121102807-C-T			Benign (Jul 05, 2018)
11-121105500-A-G			Likely benign (Jan 28, 2019)
11-121105602-A-C			Benign (Dec 21, 2018)
11-121105704-G-A			Benign (Nov 12, 2018)
11-121105719-A-G			Benign (Nov 12, 2018)
11-121105751-G-A			Likely benign (Jun 29, 2018)
11-121105812-C-T			Likely benign (Mar 04, 2023)
11-121105817-A-G		not specified • Autosomal recessive nonsyndromic hearing loss 21 • Autosomal dominant nonsyndromic hearing loss 12	Conflicting classifications of pathogenicity (Jul 27, 2023)
11-121105840-G-C		Inborn genetic diseases	Uncertain significance (Apr 19, 2023)
11-121105846-T-C		Autosomal dominant nonsyndromic hearing loss 12 • Autosomal recessive nonsyndromic hearing loss 21	Uncertain significance (Jan 12, 2018)
11-121105850-G-A		Inborn genetic diseases	Uncertain significance (Jul 30, 2023)
11-121105856-A-T		not specified • Autosomal recessive nonsyndromic hearing loss 21 • Autosomal dominant nonsyndromic hearing loss 12	Conflicting classifications of pathogenicity (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TECTA	protein_coding	protein_coding	ENST00000392793	23	90321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.99e-16	1.00	125599	1	148	125748	0.000593

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	1095	1.26e+3	0.872	0.0000817	14244
Missense in Polyphen		344	454.81	0.75636		5097
Synonymous	0.182	538	543	0.990	0.0000420	4146
Loss of Function	4.98	43	95.6	0.450	0.00000531	1060

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00111
Ashkenazi Jewish	0.000894	0.000893
East Asian	0.000873	0.000870
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000693	0.000686
Middle Eastern	0.000873	0.000870
South Asian	0.000523	0.000490
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: One of the major non-collagenous components of the tectorial membrane (By similarity). The tectorial membrane is an extracellular matrix of the inner ear that covers the neuroepithelium of the cochlea and contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. {ECO:0000250}.
• Disease: DISEASE: Deafness, autosomal dominant, 12 (DFNA12) [MIM:601543]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:10196713, ECO:0000269|PubMed:10987647, ECO:0000269|PubMed:12162770, ECO:0000269|PubMed:15319541, ECO:0000269|PubMed:16718611, ECO:0000269|PubMed:17661817, ECO:0000269|PubMed:20947814, ECO:0000269|PubMed:21520338, ECO:0000269|PubMed:9590290}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Deafness, autosomal recessive, 21 (DFNB21) [MIM:603629]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:12746400, ECO:0000269|PubMed:9949200}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.207

Intolerance Scores

• loftool: 0.229
• rvis_EVS: -2.43
• rvis_percentile_EVS: 1.03

Haploinsufficiency Scores

• pHI: 0.647
• hipred: Y
• hipred_score: 0.725
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tecta
• Phenotype: hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: tecta
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: cell-matrix adhesion;sensory perception of sound
• Cellular component: extracellular region;plasma membrane;anchored component of membrane;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent