PRCD

photoreceptor disc component

Basic information

Region (hg38): 17:76527586-76553578

Links

ENSG00000214140 ∙ NCBI:768206 ∙ OMIM:610598 ∙ HGNC:32528 ∙ Uniprot:Q00LT1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 36 (Moderate), mode of inheritance: AR
• retinitis pigmentosa 36 (Strong), mode of inheritance: AR
• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 36 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 36	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	16938425

ClinVar

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

• not_provided (87 variants)
• Retinitis_pigmentosa (13 variants)
• Inborn_genetic_diseases (10 variants)
• Retinitis_pigmentosa_36 (8 variants)
• Retinal_dystrophy (6 variants)
• not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRCD gene is commonly pathogenic or not. These statistics are base on transcript: NM_001077620.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	20		21
missense	1	1	29	1		32
nonsense	3	1				4
start loss		1				1
frameshift	2	2	1			5
splice donor/acceptor (+/-2bp)	1	3				4
Total	7	8	31	21	0

Highest pathogenic variant AF is 0.0000132296

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRCD	protein_coding	protein_coding	ENST00000586148	3	25993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0160	0.718	124770	0	14	124784	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.297	30	34.9	0.858	0.00000213	343
Missense in Polyphen		2	1.7893	1.1178		21
Synonymous	-0.344	14	12.5	1.12	7.05e-7	106
Loss of Function	0.696	3	4.61	0.650	3.68e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000196	0.000189
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000672	0.0000618
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in vision.
• Disease: DISEASE: Retinitis pigmentosa 36 (RP36) [MIM:610599]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:16938425, ECO:0000269|PubMed:24992209}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.737
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.180
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prcd

Gene ontology

• Biological process: visual perception;response to stimulus
• Cellular component: photoreceptor outer segment;extracellular region;cytoplasm;endoplasmic reticulum;Golgi apparatus