TECTA

tectorin alpha

Basic information

Region (hg38): 11:121101243-121191490

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

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

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 (917 variants)
• Inborn_genetic_diseases (303 variants)
• Autosomal_dominant_nonsyndromic_hearing_loss_12 (212 variants)
• not_specified (209 variants)
• Autosomal_recessive_nonsyndromic_hearing_loss_21 (198 variants)
• TECTA-related_disorder (66 variants)
• Hearing_impairment (17 variants)
• Nonsyndromic_genetic_hearing_loss (14 variants)
• Rare_genetic_deafness (13 variants)
• Hearing_loss,_autosomal_recessive (11 variants)
• Nonsyndromic_Hearing_Loss,_Dominant (5 variants)
• Meniere_disease (5 variants)
• Deafness,_neurosensory_autosomal_recessive_21 (3 variants)
• Ear_malformation (3 variants)
• Monogenic_hearing_loss (2 variants)
• Deafness (1 variants)
• Congenital_sensorineural_hearing_impairment (1 variants)
• See_cases (1 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Bilateral_sensorineural_hearing_impairment (1 variants)
• Sensorineural_hearing_loss_disorder (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. These statistics are base on transcript: NM_000005422.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		3	36	211	4	254
missense	6	27	704	101	4	842
nonsense	19	15	2			36
start loss						0
frameshift	25	25				50
splice donor/acceptor (+/-2bp)	4	7	2			13
Total	54	77	744	312	8

Highest pathogenic variant AF is 0.00017886198

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
		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

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

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