PRB3

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

Basic information

Region (hg38): 12:11265913-11269707

Links

ENSG00000197870 ∙ NCBI:5544 ∙ OMIM:168840 ∙ HGNC:9339 ∙ Uniprot:Q04118 ∙ 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 PRB3 gene.

• Inborn genetic diseases (22 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRB3 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				4		4
missense			19	7		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	11	0

Variants in PRB3

This is a list of pathogenic ClinVar variants found in the PRB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-11267374-G-A		not specified	Uncertain significance (Dec 01, 2022)
12-11267395-G-A		not specified	Uncertain significance (Nov 15, 2021)
12-11267400-A-AG		PRB3M(NULL)	Pathogenic (Oct 01, 1990)
12-11267418-T-G		not specified	Uncertain significance (Jul 14, 2021)
12-11267429-C-T		not specified	Uncertain significance (Jan 09, 2024)
12-11267453-T-C			Likely benign (Aug 01, 2022)
12-11267457-T-C			Likely benign (Apr 01, 2022)
12-11267692-G-T			Likely benign (Aug 01, 2023)
12-11267701-G-A		not specified	Uncertain significance (Dec 13, 2022)
12-11267719-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-11267735-G-T		not specified	Uncertain significance (Oct 05, 2023)
12-11267755-G-T		not specified	Uncertain significance (Feb 17, 2022)
12-11267781-C-T			Likely benign (Jun 01, 2023)
12-11267802-T-G			Likely benign (Sep 01, 2022)
12-11267818-G-C		not specified	Uncertain significance (Mar 21, 2022)
12-11267818-G-T		not specified	Uncertain significance (Mar 16, 2022)
12-11267839-C-T			Likely benign (Mar 01, 2024)
12-11267869-C-T		not specified	Uncertain significance (Mar 13, 2023)
12-11267912-G-T		not specified	Uncertain significance (Feb 23, 2023)
12-11267947-C-T		not specified	Uncertain significance (Oct 06, 2022)
12-11267971-G-A		not specified	Uncertain significance (Oct 16, 2023)
12-11267991-T-G			Likely benign (Apr 01, 2022)
12-11267992-C-T		not specified	Uncertain significance (Oct 12, 2022)
12-11267993-C-T		not specified	Uncertain significance (Mar 29, 2022)
12-11268067-G-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRB3	protein_coding	protein_coding	ENST00000381842	5	3883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.24e-7	0.459	125687	0	58	125745	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.993	218	180	1.21	0.0000102	1871
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00160	0.00160
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.139

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.338

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process;defense response to Gram-negative bacterium
• Cellular component: extracellular region