PCARE

photoreceptor cilium actin regulator

Basic information

Region (hg38): 2:29060975-29074523

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 (856 variants)
• Retinitis pigmentosa (226 variants)
• Retinitis pigmentosa 54 (47 variants)
• not specified (30 variants)
• Retinal dystrophy (18 variants)
• Retinitis Pigmentosa, Recessive (5 variants)
• Autosomal recessive retinitis pigmentosa (4 variants)
• PCARE-related condition (2 variants)
• Cone-rod dystrophy (2 variants)
• Cone-rod dystrophy 23 (1 variants)
• See cases (1 variants)
• PCARE-related retinopathy (1 variants)
• Stargardt disease (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.

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			10	199	11	220
missense		1	461	12	13	487
nonsense	29	5	2			36
start loss						0
frameshift	52	17	3			72
inframe indel		1	17	1	1	20
splice donor/acceptor (+/-2bp)		1				1
splice region			2	1		3
non coding			63	18	24	105
Total	81	25	556	230	49

Highest pathogenic variant AF is 0.0000329

Variants in PCARE

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

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

Position	Type	Phenotype	Significance	ClinVar
2-29061806-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-29061812-G-A		Retinitis pigmentosa	Benign (Jan 13, 2018)
2-29061819-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29061828-T-C		Retinitis pigmentosa	Likely benign (Jan 13, 2018)
2-29061829-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29061832-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29061833-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29061861-C-A		Retinitis pigmentosa	Uncertain significance (Apr 27, 2017)
2-29061940-A-G		Retinitis pigmentosa	Benign (Jan 13, 2018)
2-29062106-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-29062115-T-C		Retinitis pigmentosa	Benign (Jan 12, 2018)
2-29062199-A-G		Retinitis pigmentosa	Benign (Jan 13, 2018)
2-29062217-A-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29062220-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29062240-C-T		Retinitis pigmentosa	Benign (Oct 12, 2017)
2-29062274-T-C		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29062284-T-C		Retinitis pigmentosa	Benign (Jan 12, 2018)
2-29062285-G-A		Retinitis pigmentosa	Likely benign (Jan 13, 2018)
2-29062290-G-T		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
2-29062307-C-G		Retinitis pigmentosa	Conflicting classifications of pathogenicity (Mar 01, 2023)
2-29062311-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29062323-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29062344-C-T		Retinitis pigmentosa	Benign (Jan 12, 2018)
2-29062357-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-29062388-C-T		Retinitis pigmentosa	Benign (Jan 13, 2018)

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