PRB1

proline rich protein BstNI subfamily 1, the group of Proline rich proteins

Basic information

Region (hg38): 12:11351823-11355591

Links

ENSG00000251655 ∙ NCBI:5542 ∙ OMIM:180989 ∙ HGNC:9337 ∙ Uniprot:P04280 ∙ 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 PRB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRB1 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				1	1	2
missense			40	2		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18			18
Total	0	0	58	3	1

Variants in PRB1

This is a list of pathogenic ClinVar variants found in the PRB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-11353129-C-T		not specified	Uncertain significance (Jul 02, 2024)
12-11353135-C-G		not specified	Uncertain significance (Aug 02, 2021)
12-11353147-C-T		not specified	Uncertain significance (Sep 04, 2024)
12-11353153-G-T		not specified	Uncertain significance (Jun 02, 2023)
12-11353154-G-T		not specified	Uncertain significance (Apr 18, 2023)
12-11353182-C-G		not specified	Uncertain significance (Mar 07, 2025)
12-11353211-G-T		not specified	Uncertain significance (Apr 05, 2023)
12-11353237-C-A		not specified	Uncertain significance (Jul 31, 2024)
12-11353237-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-11353244-G-T		not specified	Uncertain significance (Sep 22, 2022)
12-11353246-T-G			Likely benign (Apr 01, 2024)
12-11353249-G-A		not specified	Uncertain significance (Nov 25, 2024)
12-11353256-C-G		not specified	Uncertain significance (Feb 01, 2025)
12-11353279-C-T		not specified	Uncertain significance (Apr 29, 2024)
12-11353294-T-A		not specified	Uncertain significance (Apr 07, 2023)
12-11353297-C-T		not specified	Uncertain significance (Oct 01, 2024)
12-11353333-G-C		not specified	Uncertain significance (Dec 22, 2023)
12-11353352-G-A		not specified	Uncertain significance (Jul 10, 2024)
12-11353352-G-T		not specified	Uncertain significance (Jan 02, 2025)
12-11353353-T-C			Likely benign (Apr 01, 2024)
12-11353355-T-G		not specified	Uncertain significance (Jan 26, 2022)
12-11353357-T-C		not specified	Uncertain significance (Nov 26, 2024)
12-11353363-C-T		not specified	Uncertain significance (Aug 13, 2021)
12-11353369-G-T		not specified	Uncertain significance (Feb 12, 2025)
12-11353372-G-A		not specified	Uncertain significance (Apr 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRB1	protein_coding	protein_coding	ENST00000500254	4	43744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.38e-11	0.0114	125010	3	30	125043	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.03	216	102	2.12	0.00000480	1195
Missense in Polyphen
Synonymous	-4.65	72	36.4	1.98	0.00000165	442
Loss of Function	-1.31	13	8.80	1.48	5.17e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000237
Ashkenazi Jewish	0.00	0.00
East Asian	0.000497	0.000490
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000265
Middle Eastern	0.000497	0.000490
South Asian	0.000533	0.000491
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Salivary secretion - Homo sapiens (human);Spinal Cord Injury (Consensus)

Intolerance Scores

• loftool: 0.986
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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
• Cellular component: extracellular region
• Molecular function: molecular_function