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 (5 variants)
• Retinal dystrophy (3 variants)
• Retinitis pigmentosa (2 variants)
• Retinitis pigmentosa 36 (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.

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				18		18
missense	1		27	1		29
nonsense	3					3
start loss		1				1
frameshift	2		1			3
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			4	3		7
non coding			44	22	7	73
Total	6	3	72	41	7

Highest pathogenic variant AF is 0.0000145

Variants in PRCD

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

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

Position	Type	Phenotype	Significance	ClinVar
17-76528584-C-T			Benign (Dec 31, 2019)
17-76528610-G-A		not specified	Uncertain significance (Dec 28, 2023)
17-76530983-T-C		not specified	Uncertain significance (Sep 20, 2023)
17-76531055-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-76531078-G-A		not specified	Uncertain significance (Jun 10, 2022)
17-76531128-G-T			Benign (Aug 20, 2018)
17-76531142-T-A		not specified	Uncertain significance (Nov 06, 2023)
17-76531491-A-G		not specified	Uncertain significance (May 27, 2022)
17-76531516-C-T		not specified	Uncertain significance (Dec 04, 2023)
17-76531524-G-C		not specified	Uncertain significance (Oct 06, 2024)
17-76531533-T-C		not specified	Uncertain significance (Dec 28, 2022)
17-76531558-C-T		not specified	Uncertain significance (Mar 17, 2023)
17-76531600-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-76531614-C-T		not specified	Uncertain significance (Aug 16, 2022)
17-76531631-A-T		not specified	Likely benign (Mar 14, 2024)
17-76537499-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-76537508-C-A		not specified	Uncertain significance (Apr 26, 2023)
17-76537515-T-C		not specified	Uncertain significance (Aug 05, 2024)
17-76537519-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-76537527-C-T		not specified	Uncertain significance (Mar 13, 2023)
17-76540048-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
17-76540060-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
17-76540143-T-C		Retinitis pigmentosa • Retinitis pigmentosa 36 • Retinal dystrophy	Pathogenic/Likely pathogenic (Oct 01, 2023)
17-76540146-G-A		Retinitis pigmentosa 36	Uncertain significance (Aug 04, 2023)
17-76540148-A-G		Inborn genetic diseases	Uncertain significance (Oct 09, 2024)

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