CABP2
geneOn this page
Summary
CABP2 (calcium binding protein 2, HGNC:1385) is a protein-coding gene on chromosome 11q13.2, encoding Calcium-binding protein 2 (Q9NPB3). Required for sound encoding at inner hair cells (IHCs) synapses, likely via inhibition of the inactivation of voltage-gated calcium channel of type 1.3 (Cav1.3) in the IHCs.
This gene belongs to a subfamily of calcium binding proteins that share similarity to calmodulin. Like calmodulin, these family members can likely stimulate calmodulin-dependent kinase II and the protein phosphatase calcineurin. Calcium binding proteins are an important component of calcium mediated cellular signal transduction. Two transcript variants encoding different isoforms have been found for this gene.
Source: NCBI Gene 51475 — RefSeq curated summary.
At a glance
- Gene–disease (curated): nonsyndromic genetic hearing loss (Definitive, ClinGen) — +2 more curated relationships
- GWAS associations: 1
- Clinical variants (ClinVar): 143 total — 2 pathogenic, 8 likely-pathogenic
- Phenotypes (HPO): 3
- Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
- MANE Select transcript:
NM_016366
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:1385 |
| Approved symbol | CABP2 |
| Name | calcium binding protein 2 |
| Location | 11q13.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000167791 |
| Ensembl biotype | protein_coding |
| OMIM | 607314 |
| Entrez | 51475 |
Gene structure
Transcript identifiers
Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay
ENST00000294288, ENST00000353903, ENST00000545205, ENST00000636477
RefSeq mRNA: 2 — MANE Select: NM_016366
NM_001318496, NM_016366
CCDS: CCDS8170
Canonical transcript exons
ENST00000294288 — 7 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001064172 | 67522546 | 67522716 |
| ENSE00002288874 | 67518912 | 67519164 |
| ENSE00003475477 | 67519793 | 67519940 |
| ENSE00003526118 | 67520051 | 67520160 |
| ENSE00003535704 | 67521025 | 67521159 |
| ENSE00003580948 | 67521952 | 67521982 |
| ENSE00003890089 | 67523285 | 67523446 |
Expression profiles
Bgee: expression breadth broad, 13 present calls, max score 72.32.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0257 / max 16.8273, expressed in 5 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 120951 | 0.0257 | 5 |
Top tissues by expression
249 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| parotid gland | UBERON:0001831 | 72.32 | gold quality |
| myocardium | UBERON:0002349 | 62.03 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 61.91 | gold quality |
| periodontal ligament | UBERON:0008266 | 60.92 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 60.19 | gold quality |
| biceps brachii | UBERON:0001507 | 59.93 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 59.22 | gold quality |
| heart right ventricle | UBERON:0002080 | 57.89 | gold quality |
| cerebellar vermis | UBERON:0004720 | 57.37 | silver quality |
| vastus lateralis | UBERON:0001379 | 56.59 | gold quality |
| quadriceps femoris | UBERON:0001377 | 56.53 | gold quality |
| cartilage tissue | UBERON:0002418 | 54.09 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 54.00 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 53.64 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 53.56 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 52.95 | gold quality |
| buccal mucosa cell | CL:0002336 | 51.54 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 51.11 | gold quality |
| body of tongue | UBERON:0011876 | 50.39 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 50.04 | gold quality |
| seminal vesicle | UBERON:0000998 | 49.69 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 49.43 | silver quality |
| blood vessel layer | UBERON:0004797 | 49.29 | gold quality |
| skeletal muscle tissue | UBERON:0001134 | 49.23 | gold quality |
| choroid plexus epithelium | UBERON:0003911 | 48.89 | gold quality |
| nephron tubule | UBERON:0001231 | 48.39 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 47.24 | gold quality |
| mammalian vulva | UBERON:0000997 | 47.23 | gold quality |
| renal glomerulus | UBERON:0000074 | 46.86 | gold quality |
| metanephric glomerulus | UBERON:0004736 | 46.77 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-7316 | yes | 698.32 |
| E-ANND-3 | no | 1.22 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
18 targeting CABP2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-4531 | 99.99 | 69.70 | 3181 |
| HSA-MIR-6825-5P | 99.96 | 69.81 | 3431 |
| HSA-MIR-6842-5P | 99.80 | 67.54 | 1587 |
| HSA-MIR-7110-5P | 99.80 | 67.84 | 1712 |
| HSA-MIR-92A-2-5P | 99.75 | 67.01 | 2164 |
| HSA-MIR-3175 | 99.65 | 66.30 | 2031 |
| HSA-MIR-4516 | 99.61 | 67.78 | 3390 |
| HSA-MIR-6752-5P | 99.59 | 67.32 | 1243 |
| HSA-MIR-12131 | 99.48 | 68.72 | 1673 |
| HSA-MIR-4434 | 99.10 | 67.01 | 1984 |
| HSA-MIR-5703 | 99.10 | 67.09 | 2053 |
| HSA-MIR-6830-5P | 99.01 | 68.73 | 1884 |
| HSA-MIR-561-5P | 98.25 | 68.13 | 1365 |
| HSA-MIR-6882-3P | 98.23 | 67.01 | 1119 |
| HSA-MIR-939-5P | 97.10 | 65.80 | 1579 |
| HSA-MIR-1343-5P | 96.48 | 66.06 | 1506 |
| HSA-MIR-541-3P | 96.07 | 66.11 | 1271 |
| HSA-MIR-654-5P | 96.07 | 66.18 | 1280 |
Functional genomics
ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map
Literature-anchored findings (GeneRIF, showing 2)
- Genetic defects in CABP2 cause moderate-to-severe sensorineural hearing impairment. (PMID:22981119)
- Autosomal recessive nonsyndromic hearing impairment in two Finnish families due to the population enriched CABP2 c.637+1G>T variant. (PMID:35150090)
Cross-species orthologs
16 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | cabp4 | ENSDARG00000008866 |
| mus_musculus | Cabp2 | ENSMUSG00000024857 |
| rattus_norvegicus | Cabp2 | ENSRNOG00000018339 |
| drosophila_melanogaster | TpnC4 | FBGN0033027 |
| drosophila_melanogaster | CG13526 | FBGN0034774 |
| drosophila_melanogaster | CG5024 | FBGN0039373 |
| drosophila_melanogaster | CG17770 | FBGN0039374 |
| drosophila_melanogaster | CG30378 | FBGN0050378 |
| caenorhabditis_elegans | WBGENE00000285 | |
| caenorhabditis_elegans | WBGENE00000287 | |
| caenorhabditis_elegans | pat-10 | WBGENE00003934 |
| caenorhabditis_elegans | WBGENE00006583 | |
| caenorhabditis_elegans | WBGENE00008453 | |
| caenorhabditis_elegans | F35C12.3 | WBGENE00009408 |
| caenorhabditis_elegans | WBGENE00015264 | |
| caenorhabditis_elegans | WBGENE00019352 |
Paralogs (20): CABP7 (ENSG00000100314), CABP5 (ENSG00000105507), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CETN3 (ENSG00000153140), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CALML6 (ENSG00000169885), EFCAB3 (ENSG00000172421), EFCAB12 (ENSG00000172771), CABP4 (ENSG00000175544), CETN1 (ENSG00000177143), CALML3 (ENSG00000178363), CALML5 (ENSG00000178372), CALN1 (ENSG00000183166), CALM1 (ENSG00000198668), EFCAB2 (ENSG00000203666), EFCAB7 (ENSG00000203965), EFCAB9 (ENSG00000214360)
Protein
Protein identifiers
Calcium-binding protein 2 — Q9NPB3 (reviewed: Q9NPB3)
All UniProt accessions (3): A0A1B0GW24, Q9NPB3, F5H458
UniProt curated annotations — full annotation on UniProt →
Function. Required for sound encoding at inner hair cells (IHCs) synapses, likely via inhibition of the inactivation of voltage-gated calcium channel of type 1.3 (Cav1.3) in the IHCs. Required for the normal transfer of light signals through the retina.
Subcellular location. Cytoplasm. Perinuclear region. Cell membrane. Golgi apparatus.
Tissue specificity. Retina.
Disease relevance. Deafness, autosomal recessive, 93 (DFNB93) [MIM:614899] A form of non-syndromic deafness characterized by stable, bilateral, symmetric, prelingual moderate to severe deafness. Hearing impairment is slightly more pronounced in the mid-frequencies, resulting in a distinctive shallow U-shaped audiogram. The disease is caused by variants affecting the gene represented in this entry.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9NPB3-1 | L-CaBP2 | yes |
| Q9NPB3-2 | S-CaBP2 |
RefSeq proteins (2): NP_001305425, NP_057450* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002048 | EF_hand_dom | Domain |
| IPR011992 | EF-hand-dom_pair | Homologous_superfamily |
| IPR018247 | EF_Hand_1_Ca_BS | Binding_site |
| IPR043582 | CaBP1/2/4/5 | Family |
Pfam: PF13499
UniProt features (26 total): binding site 14, domain 4, sequence variant 2, initiator methionine 1, chain 1, lipid moiety-binding region 1, splice variant 1, region of interest 1, compositionally biased region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NPB3-F1 | 68.93 | 0.13 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (14): 95; 97; 102; 165; 167; 169; 171; 176; 202; 204; 206; 213 …
Post-translational modifications (1): 2
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-9662360 | Sensory processing of sound by inner hair cells of the cochlea |
| R-HSA-9659379 | Sensory processing of sound |
| R-HSA-9709957 | Sensory Perception |
MSigDB gene sets: 68 (showing top):
RNGTGGGC_UNKNOWN, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_PHOTOTRANSDUCTION, chr11q13, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_RADIATION, GOBP_DETECTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, GOBP_RESPONSE_TO_LIGHT_STIMULUS, AP4_01, NFAT_Q6
GO Biological Process (3): signal transduction (GO:0007165), visual perception (GO:0007601), sensory perception of sound (GO:0007605)
GO Molecular Function (4): calcium channel regulator activity (GO:0005246), calcium ion binding (GO:0005509), protein binding (GO:0005515), metal ion binding (GO:0046872)
GO Cellular Component (5): cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), perinuclear region of cytoplasm (GO:0048471), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Sensory processing of sound | 1 |
| Sensory Perception | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| cytoplasm | 2 |
| cell communication | 1 |
| cellular process | 1 |
| signaling | 1 |
| regulation of cellular process | 1 |
| cellular response to stimulus | 1 |
| sensory perception of light stimulus | 1 |
| sensory perception of mechanical stimulus | 1 |
| calcium channel activity | 1 |
| ion channel regulator activity | 1 |
| metal ion binding | 1 |
| binding | 1 |
| cation binding | 1 |
| intracellular anatomical structure | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| membrane | 1 |
| cell periphery | 1 |
Protein interactions and networks
STRING
1669 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CABP2 | S100G | P29377 | 748 |
| CABP2 | CACNA1F | O60840 | 622 |
| CABP2 | GRK5 | P34947 | 594 |
| CABP2 | CACNA1D | Q01668 | 554 |
| CABP2 | OTOF | Q9HC10 | 496 |
| CABP2 | STRC | Q7RTU9 | 491 |
| CABP2 | SMOC2 | Q9H3U7 | 487 |
| CABP2 | GRXCR2 | A6NFK2 | 478 |
| CABP2 | OTOG | Q6ZRI0 | 468 |
| CABP2 | PJVK | Q0ZLH3 | 460 |
| CABP2 | OR2T5 | Q6IEZ7 | 447 |
| CABP2 | NCS1 | P36610 | 442 |
| CABP2 | TMIE | Q8NEW7 | 433 |
| CABP2 | GRXCR1 | A8MXD5 | 426 |
| CABP2 | ILDR1 | Q86SU0 | 426 |
IntAct
110 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CABP2 | NOP10 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | AVPI1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | ADGRF5 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | MXRA8 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | COA6 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| CABP2 | ZNF785 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | ZNF140 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | NME4 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | C22orf39 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOXD12 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| EFHC2 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| CARD9 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| GOLGA6L9 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOOK2 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UNKL | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| THAP6 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ZNF57 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| AVPI1 | CABP2 | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (61): CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid), CABP2 (Two-hybrid)
ESM2 similar proteins: A4Q9F3, A8IHN8, D3YYI7, M0R7T9, O09112, O60347, O88751, P51509, Q09YL6, Q0IHH1, Q13202, Q13505, Q14190, Q147X3, Q17QD9, Q3TZ87, Q3UPL5, Q3V1H9, Q5TGI4, Q5VUJ9, Q5VV17, Q5XI57, Q61079, Q6A039, Q6PDS0, Q6ZVT0, Q7Z7K6, Q80UW0, Q86YJ5, Q8C4U2, Q8CES0, Q8N554, Q8N8J7, Q8TC41, Q8TDR2, Q8WWW0, Q96AQ8, Q96ET8, Q96KN8, Q96MM7
Diamond homologs: A8CEP3, D2DGW3, O16305, O60041, O88751, O94739, O96102, P02585, P02586, P02587, P02588, P02589, P02597, P02598, P02599, P04464, P05419, P05933, P06707, P06708, P06787, P07463, P10246, P11118, P11120, P11121, P15094, P15159, P18061, P20801, P23286, P24044, P25071, P27165, P27166, P29290, P29291, P47947, P47948, P47949
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
143 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 2 |
| Likely pathogenic | 8 |
| Uncertain significance | 67 |
| Likely benign | 47 |
| Benign | 9 |
Top pathogenic / likely-pathogenic (10)
| Variant ID | HGVS | Classification |
|---|---|---|
| 3340148 | NM_016366.3(CABP2):c.274C>T (p.Arg92Ter) | Pathogenic |
| 917515 | NM_016366.3(CABP2):c.232G>A (p.Glu78Lys) | Pathogenic |
| 1324001 | NM_016366.3(CABP2):c.482del (p.Phe161fs) | Likely pathogenic |
| 1698683 | NM_016366.3(CABP2):c.490-8C>A | Likely pathogenic |
| 2057154 | NM_016366.3(CABP2):c.42+1G>C | Likely pathogenic |
| 2664943 | NM_016366.3(CABP2):c.60C>A (p.Leu20=) | Likely pathogenic |
| 2895007 | NM_016366.3(CABP2):c.213+1G>A | Likely pathogenic |
| 3898887 | NM_016366.3(CABP2):c.547del (p.Ala183fs) | Likely pathogenic |
| 4684997 | NM_016366.3(CABP2):c.245-1G>A | Likely pathogenic |
| 817309 | NM_016366.2(CABP2):c.638_639delAG | Likely pathogenic |
SpliceAI
1316 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 11:67519831:T:TA | donor_gain | 1.0000 |
| 11:67521023:A:AC | donor_gain | 1.0000 |
| 11:67521024:C:CC | donor_gain | 1.0000 |
| 11:67521158:CT:C | acceptor_gain | 1.0000 |
| 11:67521160:C:CC | acceptor_gain | 1.0000 |
| 11:67519335:T:C | acceptor_gain | 0.9900 |
| 11:67520052:T:TA | donor_gain | 0.9900 |
| 11:67520053:C:A | donor_gain | 0.9900 |
| 11:67520159:ACC:A | acceptor_loss | 0.9900 |
| 11:67520162:T:A | acceptor_loss | 0.9900 |
| 11:67521024:CTG:C | donor_gain | 0.9900 |
| 11:67521024:CTGA:C | donor_gain | 0.9900 |
| 11:67521024:CTGAT:C | donor_gain | 0.9900 |
| 11:67521155:CAGCT:C | acceptor_gain | 0.9900 |
| 11:67521156:A:T | acceptor_gain | 0.9900 |
| 11:67521156:AGCT:A | acceptor_gain | 0.9900 |
| 11:67521159:TC:T | acceptor_loss | 0.9900 |
| 11:67521161:T:C | acceptor_loss | 0.9900 |
| 11:67522541:CATA:C | donor_gain | 0.9900 |
| 11:67522544:A:AC | donor_gain | 0.9900 |
| 11:67522545:C:CC | donor_gain | 0.9900 |
| 11:67519335:T:TC | acceptor_gain | 0.9800 |
| 11:67519743:T:C | donor_gain | 0.9800 |
| 11:67519941:C:CC | acceptor_gain | 0.9800 |
| 11:67520158:CAC:C | acceptor_gain | 0.9800 |
| 11:67520171:C:T | acceptor_gain | 0.9800 |
| 11:67521021:ATAC:A | donor_loss | 0.9800 |
| 11:67521022:TA:T | donor_loss | 0.9800 |
| 11:67521164:C:CT | acceptor_gain | 0.9800 |
| 11:67522540:A:AC | donor_gain | 0.9800 |
AlphaMissense
1432 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 11:67521048:A:G | L119P | 0.998 |
| 11:67521063:G:T | P114H | 0.998 |
| 11:67521134:A:C | F90L | 0.998 |
| 11:67521134:A:T | F90L | 0.998 |
| 11:67521136:A:G | F90L | 0.998 |
| 11:67521143:G:C | F87L | 0.998 |
| 11:67521143:G:T | F87L | 0.998 |
| 11:67521145:A:G | F87L | 0.998 |
| 11:67519915:A:G | I172T | 0.997 |
| 11:67520057:G:C | F161L | 0.997 |
| 11:67520057:G:T | F161L | 0.997 |
| 11:67520059:A:G | F161L | 0.997 |
| 11:67520133:A:G | F136S | 0.997 |
| 11:67521144:A:G | F87S | 0.997 |
| 11:67519160:A:C | F214L | 0.996 |
| 11:67519160:A:T | F214L | 0.996 |
| 11:67519162:A:G | F214L | 0.996 |
| 11:67519915:A:T | I172N | 0.996 |
| 11:67520058:A:G | F161S | 0.996 |
| 11:67520124:A:G | L139P | 0.996 |
| 11:67520132:G:C | F136L | 0.996 |
| 11:67520132:G:T | F136L | 0.996 |
| 11:67520134:A:G | F136L | 0.996 |
| 11:67521063:G:C | P114R | 0.996 |
| 11:67521081:C:G | R108P | 0.996 |
| 11:67521111:A:T | I98N | 0.996 |
| 11:67521156:A:G | L83P | 0.996 |
| 11:67519900:A:G | L177P | 0.995 |
| 11:67520070:A:G | L157P | 0.995 |
| 11:67521064:G:A | P114S | 0.995 |
dbSNP variants (sampled 300 via entrez): RS1000010545 (11:67521486 A>T), RS1000600618 (11:67525250 C>A), RS1000908049 (11:67525411 G>A), RS1002203521 (11:67518551 C>G,T), RS1002622086 (11:67522928 C>T), RS1002821097 (11:67521282 C>T), RS1002980284 (11:67523164 C>T), RS1003831530 (11:67524782 T>C), RS1003967721 (11:67523715 G>A), RS1004170605 (11:67524181 C>T), RS1004474836 (11:67518578 G>A), RS1005009026 (11:67521892 A>C,T), RS1005585326 (11:67523108 C>T), RS1006122126 (11:67519724 C>G), RS1006364915 (11:67524556 TC>T)
Disease associations
OMIM: gene MIM:607314 | disease phenotypes: MIM:614899, MIM:209850, MIM:220290, MIM:607197
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| nonsyndromic genetic hearing loss | Definitive | Autosomal recessive |
| autosomal recessive nonsyndromic hearing loss 93 | Strong | Autosomal recessive |
| hearing loss, autosomal recessive | Supportive | Autosomal recessive |
ClinGen Gene-Disease Validity (1)
Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.
| Disease | Classification | Inheritance |
|---|---|---|
| nonsyndromic genetic hearing loss | Definitive | AR |
Mondo (5): hearing loss disorder (MONDO:0005365), autosomal recessive nonsyndromic hearing loss 93 (MONDO:0013963), autism (MONDO:0005260), hearing loss, autosomal recessive (MONDO:0019588), nonsyndromic genetic hearing loss (MONDO:0019497)
Orphanet (3): Rare autosomal recessive non-syndromic sensorineural deafness type DFNB (Orphanet:90636), Rare autosomal dominant non-syndromic sensorineural deafness type DFNA (Orphanet:90635), Rare non-syndromic genetic deafness (Orphanet:87884)
HPO phenotypes
3 total (4 of 3 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000365 | Hearing impairment |
| HP:0003577 | Congenital onset |
| HP:0000717 | Autism |
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST010002_241 | Refractive error | 3.000000e-13 |
MeSH disease descriptors (4)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D001321 | Autistic Disorder | F03.625.164.113.500 |
| D034381 | Hearing Loss | C09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341 |
| C564609 | Deafness, Autosomal Recessive (supp.) | |
| C580334 | Nonsyndromic Deafness (supp.) |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
5 total (human), top 5 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation | 2 |
| pirinixic acid | affects binding, decreases expression, increases activity | 1 |
| bisphenol S | decreases methylation | 1 |
| Rotenone | decreases expression | 1 |
| Valproic Acid | increases methylation | 1 |
Clinical trials (associated diseases)
301 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00205881 | PHASE4 | COMPLETED | Bilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System |
| NCT00331539 | PHASE4 | UNKNOWN | Relationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant |
| NCT00424307 | PHASE4 | UNKNOWN | Bilateral Cochlear Implant Benefit in Young Children |
| NCT00765635 | PHASE4 | COMPLETED | Chlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal |
| NCT03321006 | PHASE4 | COMPLETED | Treating Hearing Loss to Improve Mood and Cognition in Older Adults |
| NCT01499901 | PHASE3 | WITHDRAWN | Comparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children |
| NCT02561091 | PHASE3 | COMPLETED | AM-111 in the Treatment of Acute Inner Ear Hearing Loss |
| NCT03331627 | PHASE3 | COMPLETED | Safety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL |
| NCT05532657 | PHASE3 | ACTIVE_NOT_RECRUITING | ACHIEVE Brain Health Follow-Up Study |
| NCT00013455 | PHASE2 | COMPLETED | Quantifying Auditory Perceptual Learning Following Hearing Aid Fitting |
| NCT00323427 | PHASE2 | COMPLETED | Clinical Trial of the Living Well With Hearing Loss Workshop |
| NCT00552786 | PHASE2 | COMPLETED | Antioxidation Medication for Noise-induced Hearing Loss |
| NCT00802425 | PHASE2 | COMPLETED | Efficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss |
| NCT01139281 | PHASE2 | COMPLETED | The Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans |
| NCT01451853 | PHASE2 | UNKNOWN | SPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss |
| NCT01588925 | PHASE2 | COMPLETED | Hearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation |
| NCT01773278 | PHASE2 | RECRUITING | Cholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS) |
| NCT02832128 | PHASE2 | COMPLETED | Evaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire) |
| NCT04915183 | PHASE2 | RECRUITING | Atorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer |
| NCT05258773 | PHASE2 | COMPLETED | Evaluation of the Presence of SENS-401 in the Perilymph |
| NCT06340633 | PHASE2 | RECRUITING | SPI-1005 in Adults Receiving Cochlear Implant |
| NCT00582946 | PHASE1 | COMPLETED | Wide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding |
| NCT00584155 | PHASE1 | WITHDRAWN | Protection From Cisplatin Ototoxicity by Lactated Ringers |
| NCT01206829 | PHASE1 | UNKNOWN | Hearing Impairment, Cognitive Therapy and Coping |
| NCT01256229 | PHASE1 | COMPLETED | Outcomes In Children With Developmental Delay And Deafness |
| NCT01343394 | PHASE1 | WITHDRAWN | Safety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children |
| NCT01452607 | PHASE1 | COMPLETED | Study to Evaluate the Safety and Pharmacokinetics of SPI-1005 |
| NCT02259595 | PHASE1 | COMPLETED | Study to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC |
| NCT04041440 | PHASE1 | COMPLETED | Speech Recognition Training in Children With Hearing Loss |
| NCT07218913 | PHASE1 | RECRUITING | Testing the Addition of Pedmark to Cisplatin Chemotherapy for Reducing Drug-Induced Ear Damage in Men With Stage II-III Metastatic Testicular Germ Cell Tumors |
| NCT01802190 | Not specified | TERMINATED | Prevalence of POU4F3 and SLC17A8 Mutations |
| NCT00486577 | PHASE2/PHASE3 | COMPLETED | Chronic Electrical Stimulation of the Auditory Cortex for Intractable Tinnitus |
| NCT00789061 | PHASE2/PHASE3 | UNKNOWN | Applying Proton Pump Inhibitor to Prevent and Treat Acute Fluctuating Hearing Loss in Patients With SLC26A4 Mutation |
| NCT01423409 | PHASE2/PHASE3 | COMPLETED | Multicenter Trial Assessing an Innovative VAS of Pain Among Deaf People |
| NCT05786378 | PHASE2/PHASE3 | UNKNOWN | Assessment of The Efficacy of Intratympanic Platelet Rich Plasma for Treatment of Sensorineural Hearing Loss. |
| NCT01108601 | PHASE1/PHASE2 | UNKNOWN | Transtympanic Ringer’s Lactate for the Prevention of Cisplatin Ototoxicity |
| NCT01621256 | PHASE1/PHASE2 | COMPLETED | Efficacy, Safety, and Tolerability of Ancrod in Patients With Sudden Hearing Loss |
| NCT06370351 | PHASE1/PHASE2 | RECRUITING | A Phase I/II Clinical Trial with SENS-501 in Children Suffering from Severe to Profound Hearing Loss Due to Otoferlin (OTOF) Mutations |
| NCT06545175 | PHASE1/PHASE2 | RECRUITING | Intracochlear Application of VSF1.01 for the Reduction of Cochlear Implant Surgery Related Trauma |
| NCT07304024 | PHASE1/PHASE2 | RECRUITING | A Treatment for a Form of Age-Related Central Auditory Processing Disorder Consisting of Clemastine Fumarate Plus Engineered Sound |
Related Atlas pages
- Associated diseases: nonsyndromic genetic hearing loss, autosomal recessive nonsyndromic hearing loss 93, hearing loss, autosomal recessive
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): autism, autosomal recessive nonsyndromic hearing loss 93, hearing loss disorder, hearing loss, autosomal recessive, nonsyndromic genetic hearing loss