PRR4

proline rich 4

Basic information

Region (hg38): 12:10845849-10849475

Previous symbols: [ "PROL4" ]

Links

ENSG00000111215 ∙ NCBI:11272 ∙ OMIM:605359 ∙ HGNC:18020 ∙ Uniprot:Q16378 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRR4 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						0
missense			10		2	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	10	0	2

Variants in PRR4

This is a list of pathogenic ClinVar variants found in the PRR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10847042-T-G		PRR4-related disorder	Likely benign (Jun 21, 2019)
12-10847101-T-C		not specified	Uncertain significance (Jun 24, 2022)
12-10847109-T-C		PRR4-related disorder	Benign (Oct 17, 2019)
12-10847115-A-G		not specified	Uncertain significance (Aug 08, 2023)
12-10847154-G-T		not specified	Uncertain significance (Apr 18, 2023)
12-10847160-G-C		not specified	Uncertain significance (Feb 28, 2023)
12-10847170-G-A		not specified	Uncertain significance (Jan 02, 2024)
12-10847178-C-T		not specified	Uncertain significance (Aug 12, 2022)
12-10847181-C-T		PRR4-related disorder	Benign (Oct 17, 2019)
12-10847190-C-G		not specified	Uncertain significance (May 26, 2023)
12-10847209-G-C		not specified	Uncertain significance (Nov 21, 2023)
12-10847214-G-C		not specified	Uncertain significance (Mar 07, 2024)
12-10848399-A-T		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRR4	protein_coding	protein_coding	ENST00000228811	3	346654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0442	0.684	116551	0	4	116555	0.0000172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.141	75	71.6	1.05	0.00000361	844
Missense in Polyphen		3	5.9356	0.50543		66
Synonymous	-0.476	28	25.0	1.12	0.00000108	287
Loss of Function	0.556	2	3.05	0.656	1.29e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000238	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0333

Intolerance Scores

• loftool: 0.703
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.0380
• hipred: N
• hipred_score: 0.146
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.180

Gene Damage Prediction

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

Gene ontology

• Biological process: retina homeostasis;visual perception
• Cellular component: extracellular space