RCVRN

recoverin, the group of EF-hand domain containing

Basic information

Region (hg38): 17:9896320-9905271

Previous symbols: [ "RCV1" ]

Links

ENSG00000109047 ∙ NCBI:5957 ∙ OMIM:179618 ∙ HGNC:9937 ∙ Uniprot:P35243 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCVRN 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						0
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in RCVRN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-9898195-G-A		not specified	Uncertain significance (Aug 21, 2024)
17-9901082-T-C			Benign (May 18, 2018)
17-9904872-C-A		not specified	Uncertain significance (Jul 27, 2024)
17-9904874-C-G		not specified	Uncertain significance (Oct 14, 2023)
17-9904910-G-A		not specified	Uncertain significance (Apr 13, 2023)
17-9904949-C-G		not specified	Uncertain significance (Feb 26, 2024)
17-9905017-T-G		not specified	Uncertain significance (Jan 31, 2023)
17-9905053-C-T		not specified	Uncertain significance (Jun 30, 2023)
17-9905087-A-G		not specified	Uncertain significance (Dec 13, 2023)
17-9905092-G-A		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCVRN	protein_coding	protein_coding	ENST00000226193	3	9302

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-9	0.0346	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.254	114	122	0.935	0.00000747	1334
Missense in Polyphen		54	58.542	0.92241		626
Synonymous	-0.118	59	57.9	1.02	0.00000461	359
Loss of Function	-0.760	12	9.48	1.27	5.73e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000453	0.000452
Ashkenazi Jewish	0.00	0.00
East Asian	0.000985	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000985	0.000979
South Asian	0.000200	0.000196
Other	0.000503	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be implicated in the pathway from retinal rod guanylate cyclase to rhodopsin. May be involved in the inhibition of the phosphorylation of rhodopsin in a calcium-dependent manner. The calcium-bound recoverin prolongs the photoresponse.
• Pathway: Phototransduction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;visual signal transduction;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.321

Intolerance Scores

• loftool: 0.682
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.335

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcvrn
• Phenotype: vision/eye phenotype

Zebrafish Information Network

• Gene name: rcvrn3
• Affected structure: cone photoresponse recovery
• Phenotype tag: abnormal
• Phenotype quality: increased efficacy

Gene ontology

• Biological process: signal transduction;visual perception;phototransduction;positive regulation of guanylate cyclase activity;regulation of calcium ion transport
• Cellular component: dendrite
• Molecular function: calcium ion binding;calcium sensitive guanylate cyclase activator activity