CABP2

calcium binding protein 2, the group of EF-hand domain containing

Basic information

Region (hg38): 11:67518912-67524517

Previous symbols: [ "DFNB93" ]

Links

ENSG00000167791 ∙ NCBI:51475 ∙ OMIM:607314 ∙ HGNC:1385 ∙ Uniprot:Q9NPB3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 93 (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 93 (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 93	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	22981119; 21542834

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CABP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABP2 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				13		13
missense			38	3	2	43
nonsense			1			1
start loss			1			1
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)		2	1			3
splice region		1	2	3	1	7
non coding		1		15	6	22
Total	0	5	41	31	8

Variants in CABP2

This is a list of pathogenic ClinVar variants found in the CABP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67519143-C-T		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
11-67519148-C-T			Likely benign (Oct 22, 2023)
11-67519155-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
11-67519156-G-A			Uncertain significance (Oct 05, 2022)
11-67519162-ACT-A			Likely pathogenic (Nov 23, 2018)
11-67519174-C-T		not specified	Likely benign (Jan 29, 2024)
11-67519197-T-C			Benign (Jun 29, 2018)
11-67519782-G-A			Likely benign (Aug 04, 2023)
11-67519786-G-C			Benign (Aug 11, 2023)
11-67519787-G-A			Uncertain significance (Mar 18, 2022)
11-67519789-G-A			Uncertain significance (Jul 18, 2022)
11-67519792-C-A		Autosomal recessive nonsyndromic hearing loss 93 • Hearing loss, autosomal recessive • CABP2-related disorder	Pathogenic/Likely pathogenic (Mar 26, 2024)
11-67519811-C-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
11-67519820-T-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
11-67519840-A-G		not specified • Autosomal recessive nonsyndromic hearing loss 93	Conflicting classifications of pathogenicity (Apr 12, 2024)
11-67519844-C-T			Uncertain significance (Aug 17, 2023)
11-67519867-C-T		Inborn genetic diseases	Uncertain significance (Jun 28, 2023)
11-67519883-C-T			Uncertain significance (Nov 01, 2022)
11-67519905-G-C			Likely benign (Jan 02, 2024)
11-67519910-C-T			Uncertain significance (Jan 07, 2022)
11-67519914-G-A			Conflicting classifications of pathogenicity (Oct 04, 2024)
11-67519916-T-A			Uncertain significance (Sep 27, 2023)
11-67519920-G-A			Likely benign (Oct 17, 2023)
11-67519937-C-A			Uncertain significance (Jun 14, 2022)
11-67519940-ACTGTGGCGGCGTTGGTTGTGGCGT-A			Uncertain significance (Feb 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABP2	protein_coding	protein_coding	ENST00000294288	7	4517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00254	0.938	125474	0	273	125747	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0294	152	153	0.993	0.0000111	1410
Missense in Polyphen		69	78.605	0.87781		669
Synonymous	-0.481	71	66.0	1.08	0.00000487	454
Loss of Function	1.64	6	12.2	0.492	6.99e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000938	0.000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00343	0.00342
European (Non-Finnish)	0.00109	0.00109
Middle Eastern	0.00	0.00
South Asian	0.00163	0.00163
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: 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 (PubMed:28183797). Required for the normal transfer of light signals through the retina (By similarity). {ECO:0000250|UniProtKB:Q9JLK4, ECO:0000269|PubMed:28183797}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.434
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.0850
• hipred: N
• hipred_score: 0.292
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.678

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabp2
• Phenotype: vision/eye 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)

Gene ontology

• Biological process: signal transduction;visual perception;sensory perception of sound
• Cellular component: Golgi apparatus;plasma membrane;perinuclear region of cytoplasm
• Molecular function: calcium channel regulator activity;calcium ion binding