PRCD

protein-coding

photoreceptor disc component

Gene summary

This gene is predominantly expressed in the retina, and mutations in this gene are the cause of autosomal recessive retinal degeneration in both humans and dogs. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2010]

MANE transcript

NM_001077620.3

Inheritance

AR, AD

ClinVar variants

P:14U:32B:23

Top phenotype

Retinitis pigmentosa 36

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr17:76,527,586-76,553,578

External References & Databases

Ensembl (ENSG00000214140)

Transcript & Mutation Effects

hg38 • Region Span ~26.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosa 36MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012523

Submitter: Ambry Genetics

retinitis pigmentosa 36STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012523

Submitter: PanelApp Australia

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

retinitis pigmentosa 36STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012523

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosa 36DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012523

Submitter: G2P

Clinical Genomic Database (CGD)

Retinitis pigmentosa 36AR

Manifestation: Ophthalmologic

Intervention: General

Rationale: 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

Refs: 16938425

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRCD variants in ClinVar

7 Conditions Cataloged

not providedTotal: 89

Retinitis pigmentosaTotal: 13

Inborn genetic diseasesTotal: 12

not specifiedTotal: 10

Retinitis pigmentosa 36Total: 10

Retinal dystrophyTotal: 5

PRCD-related disordersTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001077620.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	21 clinvar		22
missense	1 clinvar	1 clinvar	30 clinvar	2 clinvar		34
nonsense	3 clinvar					3
start loss		1 clinvar				1
frameshift	2 clinvar	2 clinvar	1 clinvar			5
splice donor/acceptor (+/-2bp)	1 clinvar	3 clinvar				4
Total	7	7	32	23	0	69

Highest pathogenic variant AF is 0.00001322963

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001077620.3	RefSeq	NP_001071088.1	3	MANE Select
ENST00000592014.6	Ensembl	ENSP00000467661.1	3	MANE Select
ENST00000586148.1	Ensembl	ENSP00000465932.1	3	Standard
ENST00000586148.2	Ensembl	ENSP00000465932.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

visual perception
response to stimulus

Cellular Component

photoreceptor outer segment
extracellular region
cytoplasm
endoplasmic reticulum
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000586148
Coding exons: 3
Length: 25993
Individuals with no LoFs: 124770
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124784
p: 0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.297	30	34.9	0.858	0.00000213	343
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000067	0.000062	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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