PCARE

photoreceptor cilium actin regulator

Basic information

Region (hg38): 2:29060976-29074523

Previous symbols: [ "C2orf71" ]

Links

ENSG00000179270 ∙ NCBI:388939 ∙ OMIM:613425 ∙ HGNC:34383 ∙ Uniprot:A6NGG8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 54 (Definitive), mode of inheritance: AR
• PCARE-related retinopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 54	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	20398884; 20398886; 20811058; 21412943; 21792230

ClinVar

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

• not_provided (909 variants)
• Retinitis_pigmentosa (120 variants)
• Retinal_dystrophy (115 variants)
• Retinitis_pigmentosa_54 (56 variants)
• PCARE-related_disorder (22 variants)
• not_specified (22 variants)
• Inborn_genetic_diseases (13 variants)
• Autosomal_recessive_retinitis_pigmentosa (5 variants)
• Cone-rod_dystrophy_23 (2 variants)
• Cone-rod_dystrophy (2 variants)
• Optic_atrophy (2 variants)
• Stargardt_disease (1 variants)
• Retinitis_pigmentosa_with_macular_involvement (1 variants)
• Retinitis_Pigmentosa,_Recessive (1 variants)
• See_cases (1 variants)
• PCARE-related_retinopathy (1 variants)
• maculopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCARE gene is commonly pathogenic or not. These statistics are base on transcript: NM_001029883.3. 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			11	263	5	279
missense		3	487	45	10	545
nonsense	42	10				52
start loss						0
frameshift	71	23	3			97
splice donor/acceptor (+/-2bp)		1				1
Total	113	37	501	308	15

Highest pathogenic variant AF is 0.0000433914

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCARE	protein_coding	protein_coding	ENST00000331664	2	13286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.01e-18	0.0612	124685	0	149	124834	0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.14	847	689	1.23	0.0000376	8378
Missense in Polyphen		160	144.52	1.1071		2066
Synonymous	-2.46	343	290	1.18	0.0000175	2667
Loss of Function	1.03	31	37.8	0.819	0.00000211	436

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00195	0.00193
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000557	0.000445
Finnish	0.00	0.00
European (Non-Finnish)	0.000509	0.000503
Middle Eastern	0.000557	0.000445
South Asian	0.000877	0.000785
Other	0.00168	0.00165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role for normal photoreceptor cell maintenance and vision. {ECO:0000269|PubMed:20398886}.

Intolerance Scores

• rvis_EVS: 1.62
• rvis_percentile_EVS: 96.02

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pcare
• Phenotype: hematopoietic system phenotype; pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: pcare
• Affected structure: photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: visual perception;photoreceptor cell outer segment organization;response to stimulus;protein localization to photoreceptor outer segment
• Cellular component: photoreceptor outer segment;photoreceptor inner segment;cilium