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

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
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 (845 variants)
Inborn_genetic_diseases (283 variants)
Autosomal_dominant_nonsyndromic_hearing_loss_12 (207 variants)
not_specified (199 variants)
Autosomal_recessive_nonsyndromic_hearing_loss_21 (194 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)
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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		3 clinvar	34 clinvar	191 clinvar	4 clinvar	232
missense	6 clinvar	26 clinvar	663 clinvar	94 clinvar	4 clinvar	793
nonsense	18 clinvar	15 clinvar	2 clinvar			35
start loss						0
frameshift	24 clinvar	23 clinvar				47
splice donor/acceptor (+/-2bp)	4 clinvar	6 clinvar				10
Total	52	73	699	285	8

Highest pathogenic variant AF is 0.00017886198

Loading clinvar variants...

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
essential_gene_gene_trap
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