PRB3

protein-coding

proline rich protein BstNI subfamily 3, the group of Proline rich proteins

Gene summary

This gene encodes a member of the heterogeneous family of basic, proline-rich, human salivary glycoproteins. Multiple alleles of this gene exhibiting variations in the length of the tandem repeats have been identified. The reference genome encodes the "Long" allele. The protein isoforms encoded by this gene are recognized as the "first line of oral defense" against the detrimental effects of polyphenols in the diet and pathogen infections. This gene is located in a cluster of closely related salivary proline-rich proteins on chromosome 12. [provided by RefSeq, Nov 2015]

MANE transcript

NM_001394862.1

Inheritance

—

ClinVar variants

P:2U:48B:17

Top phenotype

PRB3M(NULL)

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr12:11,265,914-11,269,707

External References & Databases

Ensembl (ENSG00000197870)

Transcript & Mutation Effects

hg38 • Region Span ~3.8 kb

Loading mutation effect viewer...

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 PRB3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 13

PRB3M(NULL)Total: 1

PRB3S(CYS)Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394862.1. 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			7 clinvar	8 clinvar		15
missense	1 clinvar		39 clinvar	9 clinvar		49
nonsense			1 clinvar			1
start loss						0
frameshift	1 clinvar		1 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	2	0	48	17	0	67

Highest pathogenic variant AF is 0.016515547

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394862.1	RefSeq	NP_001381791.1	3	MANE Select
ENST00000538488.3	Ensembl	ENSP00000442626.2	3	MANE Select
NM_006249.5	RefSeq	NP_006240.4	4	Standard
ENST00001141215.1	Ensembl	ENSP00000813945.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
defense response to Gram-negative bacterium

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381842
Coding exons: 5
Length: 3883
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125745
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.993	218	180	1.21	0.0000102	1871
Missense (PolyPhen)
Synonymous	-0.652	66	59.6	1.11	0.00000299	702
Loss of Function	0.728	11	13.9	0.789	7.93e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.0016	0.0016	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a receptor for the Gram-negative bacterium F.nucleatum. {ECO:0000269|PubMed:1894623}.;

Essentials

Indispensability pred.: N
Indispensability score: 0.338

Gene Damage Prediction

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