PRR4

protein-coding

proline rich 4

Gene summary

This gene encodes a member of the proline-rich protein family that lacks a conserved repetitive domain. This protein may play a role in protective functions in the eye. Alternative splicing result in multiple transcript variants. Read-through transcription also exists between this gene and the upstream PRH1 (proline-rich protein HaeIII subfamily 1) gene. [provided by RefSeq, Feb 2011]

Previous symbols:

PROL4

MANE transcript

NM_007244.3

Inheritance

—

ClinVar variants

U:18B:2

Top phenotype

PRR4-related disorder

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr12:10,845,849-10,849,475

External References & Databases

Ensembl (ENSG00000111215)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRR4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 20

PRR4-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007244.3. 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				2 clinvar		2
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	2	0	20

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007244.3	RefSeq	NP_009175.2	3	MANE Select
ENST00000228811.8	Ensembl	ENSP00000228811.4	3	MANE Select
NM_001098538.3	RefSeq	NP_001092008.2	4	Standard
ENST00000535024.7	Ensembl	ENSP00000481571.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

retina homeostasis
visual perception

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000228811
Coding exons: 3
Length: 346654
Individuals with no LoFs: 116551
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 116555
p: 0.0000172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.141	75	71.6	1.05	0.00000361	844
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00021	0.00021	rare
Latino/Admixed American	0.000033	0.000033	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0333

Intolerance Scores

LoFtool: 0.703
RVIS EVS: 0.57
RVIS percentile EVS: 81.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.180

Gene Damage Prediction

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