CABP4

calcium binding protein 4, the group of EF-hand domain containing

Basic information

Region (hg38): 11:67452405-67461752

Links

ENSG00000175544 ∙ NCBI:57010 ∙ OMIM:608965 ∙ HGNC:1386 ∙ Uniprot:P57796 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod synaptic disorder, congenital nonprogressive (Strong), mode of inheritance: AR
• congenital stationary night blindness (Supportive), mode of inheritance: AD
• autosomal dominant nocturnal frontal lobe epilepsy (Supportive), mode of inheritance: AD
• cone-rod synaptic disorder, congenital nonprogressive (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod synaptic disorder, congenital nonprogressive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	16960802; 23714322

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CABP4 gene.

• not provided (269 variants)
• Cone-rod synaptic disorder, congenital nonprogressive (110 variants)
• Congenital Stationary Night Blindness, Recessive (22 variants)
• Inborn genetic diseases (22 variants)
• not specified (4 variants)
• Retinal dystrophy (3 variants)
• Cone-rod dystrophy (2 variants)
• Congenital stationary night blindness (1 variants)
• Usher syndrome (1 variants)
• Cone dystrophy (1 variants)
• Achromatopsia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABP4 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			6	45	3	54
missense	1	1	124	7	3	136
nonsense	5	2		1		8
start loss						0
frameshift	7	2				9
inframe indel			1			1
splice donor/acceptor (+/-2bp)	3	3	2			8
splice region			6	6	5	17
non coding	1		77	19	19	116
Total	17	8	210	72	25

Highest pathogenic variant AF is 0.0000395

Variants in CABP4

This is a list of pathogenic ClinVar variants found in the CABP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67452459-A-G		not specified	Uncertain significance (May 04, 2023)
11-67452532-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-67452544-C-T		Cone-rod synaptic disorder, congenital nonprogressive	Benign (May 28, 2019)
11-67452545-A-T		not specified	Likely benign (Apr 11, 2023)
11-67452564-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-67452668-C-G		not specified	Uncertain significance (Aug 04, 2021)
11-67455134-A-C			Benign (Jul 06, 2018)
11-67455397-G-A		Cone-rod synaptic disorder, congenital nonprogressive	Uncertain significance (Jan 12, 2018)
11-67455427-A-G			Uncertain significance (Apr 24, 2021)
11-67455433-G-C		Cone-rod synaptic disorder, congenital nonprogressive • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 05, 2024)
11-67455438-G-T			Uncertain significance (Feb 19, 2022)
11-67455444-G-C			Uncertain significance (Jun 04, 2022)
11-67455447-G-A			Likely benign (Jun 09, 2021)
11-67455459-A-G			Likely benign (Jan 02, 2024)
11-67455465-G-C			Likely benign (Jan 18, 2024)
11-67455469-A-G			Uncertain significance (Feb 07, 2020)
11-67455470-T-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 12, 2022)
11-67455473-G-C			Benign (Dec 15, 2023)
11-67455475-C-T			Uncertain significance (Jul 19, 2022)
11-67455476-G-A		Cone-rod synaptic disorder, congenital nonprogressive	Benign (Jan 14, 2024)
11-67455482-A-G			Uncertain significance (May 24, 2022)
11-67455483-GC-G		Retinal dystrophy • Cone-rod synaptic disorder, congenital nonprogressive	Pathogenic/Likely pathogenic (Jun 01, 2021)
11-67455484-CC-A		Cone-rod synaptic disorder, congenital nonprogressive	Pathogenic (Jan 25, 2019)
11-67455487-C-G			Uncertain significance (Mar 12, 2021)
11-67455488-C-T			Uncertain significance (Sep 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABP4	protein_coding	protein_coding	ENST00000325656	6	6823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-10	0.0624	125690	0	40	125730	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.517	208	188	1.11	0.0000132	1749
Missense in Polyphen		61	52.653	1.1585		517
Synonymous	-0.188	82	79.9	1.03	0.00000594	583
Loss of Function	-0.0172	15	14.9	1.00	0.00000113	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000303
Ashkenazi Jewish	0.000318	0.000298
East Asian	0.000239	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000156	0.000149
Middle Eastern	0.000239	0.000163
South Asian	0.000276	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in normal synaptic function through regulation of Ca(2+) influx and neurotransmitter release in photoreceptor synaptic terminals and in auditory transmission. Modulator of CACNA1D and CACNA1F, suppressing the calcium-dependent inactivation and shifting the activation range to more hyperpolarized voltages (By similarity). {ECO:0000250}.
• Disease: DISEASE: Cone-rod synaptic disorder, congenital non-progressive (CRSD) [MIM:610427]: A non-progressive retinal disorder characterized by stable low vision, nystagmus, photophobia, a normal or near-normal fundus appearance, and no night blindness. {ECO:0000269|PubMed:16960802}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.896
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.146
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.726

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabp4
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye 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;phototransduction;photoreceptor cell morphogenesis;retinal cone cell development;retinal bipolar neuron differentiation
• Cellular component: extracellular region;cytosol;terminal bouton;synapse
• Molecular function: calcium channel regulator activity;calcium ion binding;ion channel binding