KCNV2

potassium voltage-gated channel modifier subfamily V member 2, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 9:2717510-2730037

Links

ENSG00000168263

∙ NCBI:169522 ∙ OMIM:607604 ∙ HGNC:19698 ∙ Uniprot:Q8TDN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

cone dystrophy with supernormal rod response (Strong), mode of inheritance: AR
cone dystrophy with supernormal rod response (Supportive), mode of inheritance: AR
cone dystrophy with supernormal rod response (Definitive), mode of inheritance: AR
inherited retinal dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinal cone dystrophy 3B	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	16909397

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCNV2 gene.

not_provided (640 variants)
Inborn_genetic_diseases (122 variants)
Cone_dystrophy_with_supernormal_rod_response (93 variants)
Retinal_dystrophy (43 variants)
KCNV2-related_disorder (24 variants)
not_specified (15 variants)
cone_dystrophy_with_supernormal_rod_electroretinogram (8 variants)
Cone_dystrophy (4 variants)
Cone-rod_dystrophy (2 variants)
Optic_atrophy (2 variants)
Stargardt_disease (1 variants)
Cone-rod_dystrophy_6 (1 variants)
Abnormality_of_the_nervous_system (1 variants)
Nystagmus (1 variants)
Progressive_cone_dystrophy_(without_rod_involvement) (1 variants)
Cone_dystrophy_3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNV2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000133497.4. 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			7 clinvar	178 clinvar	6 clinvar	191
missense	5 clinvar	16 clinvar	393 clinvar	39 clinvar	4 clinvar	457
nonsense	24 clinvar	10 clinvar	2 clinvar			36
start loss		1				1
frameshift	18 clinvar	7 clinvar	2 clinvar			27
splice donor/acceptor (+/-2bp)						0
Total	47	34	404	217	10

Highest pathogenic variant AF is 0.00025096885

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNV2	protein_coding	protein_coding	ENST00000382082	2	12536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-26	7.01e-7	125633	0	115	125748	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.48	606	365	1.66	0.0000280	3503
Missense in Polyphen		216	133.17	1.622		1282
Synonymous	-5.24	253	167	1.52	0.0000145	1099
Loss of Function	-3.30	31	16.5	1.88	7.28e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00134
Ashkenazi Jewish	0.00	0.00
East Asian	0.000505	0.000489
Finnish	0.000198	0.000185
European (Non-Finnish)	0.000458	0.000440
Middle Eastern	0.000505	0.000489
South Asian	0.000404	0.000392
Other	0.000679	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Potassium channel subunit. Modulates channel activity by shifting the threshold and the half-maximal activation to more negative values.;
Disease: DISEASE: Cone dystrophy retinal 3B (RCD3B) [MIM:610356]: A rare form of cone dystrophy associated with supernormal rod responses. The disorder is characterized by reduced visual acuity, photoaversion, night blindness, and abnormal color vision. At an early age, the retina shows subtle depigmentation at the macula and, later, more obvious areas of atrophy. {ECO:0000269|PubMed:16909397}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

pRec: 0.122

Intolerance Scores

loftool: 0.0969
rvis_EVS: -0.84
rvis_percentile_EVS: 11.45

Haploinsufficiency Scores

pHI: 0.451
hipred: N
hipred_score: 0.251
ghis: 0.408

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.630

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Kcnv2
Phenotype: skeleton phenotype; normal phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: regulation of ion transmembrane transport;protein homooligomerization;potassium ion transmembrane transport
Cellular component: plasma membrane;voltage-gated potassium channel complex;integral component of membrane
Molecular function: voltage-gated potassium channel activity