PRB4

proline rich protein BstNI subfamily 4, the group of Proline rich proteins

Basic information

Region (hg38): 12:11307077-11310436

Links

ENSG00000230657 ∙ NCBI:5545 ∙ OMIM:180990 ∙ HGNC:9340 ∙ Uniprot:P10163 ∙ 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 PRB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRB4 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				7		7
missense			33	1	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	33	8	2

Variants in PRB4

This is a list of pathogenic ClinVar variants found in the PRB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-11308246-G-T		not specified	Uncertain significance (Nov 29, 2023)
12-11308270-C-G		not specified	Uncertain significance (Dec 13, 2022)
12-11308279-C-T		not specified	Uncertain significance (Dec 27, 2022)
12-11308318-C-A		not specified	Uncertain significance (Aug 05, 2024)
12-11308318-C-G		not specified	Uncertain significance (Jun 28, 2024)
12-11308318-C-T		not specified	Uncertain significance (Dec 11, 2023)
12-11308330-G-C		not specified	Uncertain significance (Jan 09, 2024)
12-11308338-C-T			Likely benign (Oct 01, 2022)
12-11308352-C-T		not specified	Uncertain significance (Jul 31, 2023)
12-11308367-G-T		not specified	Uncertain significance (Dec 04, 2024)
12-11308381-C-A		not specified	Uncertain significance (Mar 04, 2024)
12-11308397-C-T		not specified	Uncertain significance (Sep 15, 2021)
12-11308403-G-T		not specified	Uncertain significance (Sep 03, 2024)
12-11308429-C-G		not specified	Uncertain significance (Jun 07, 2024)
12-11308433-G-T		not specified	Uncertain significance (Nov 15, 2024)
12-11308437-C-A		not specified	Uncertain significance (Feb 06, 2025)
12-11308439-T-C		not specified	Uncertain significance (Oct 04, 2022)
12-11308501-T-C		not specified	Uncertain significance (Sep 01, 2021)
12-11308510-T-G		not specified	Uncertain significance (Sep 16, 2021)
12-11308523-C-A		not specified	Uncertain significance (Oct 05, 2021)
12-11308535-T-A		not specified	Uncertain significance (Jul 06, 2021)
12-11308536-A-G		not specified	Likely benign (Nov 09, 2023)
12-11308536-A-T			Likely benign (May 01, 2024)
12-11308542-T-C			Likely benign (May 01, 2024)
12-11308581-G-A			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRB4	protein_coding	protein_coding	ENST00000279575	3	3353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-9	0.00798	91945	351	33452	125748	0.145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.21	234	131	1.79	0.00000645	1472
Missense in Polyphen
Synonymous	-1.69	60	45.5	1.32	0.00000196	560
Loss of Function	-2.93	10	3.82	2.62	1.63e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.195	0.194
Ashkenazi Jewish	0.112	0.117
East Asian	0.00115	0.00114
Finnish	0.179	0.195
European (Non-Finnish)	0.181	0.195
Middle Eastern	0.00115	0.00114
South Asian	0.0658	0.0673
Other	0.155	0.162

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.976
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.37

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00223

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