PRRG4

proline rich and Gla domain 4, the group of Proline rich and Gla domain containing

Basic information

Region (hg38): 11:32829926-32858120

Links

ENSG00000135378 ∙ NCBI:79056 ∙ OMIM:611690 ∙ HGNC:30799 ∙ Uniprot:Q9BZD6 ∙ 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 PRRG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRG4 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
missense			7	3	2	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	7	3	3

Variants in PRRG4

This is a list of pathogenic ClinVar variants found in the PRRG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-32830545-G-A		not specified	Likely benign (Jun 22, 2024)
11-32830590-T-G		not specified	Uncertain significance (Jun 07, 2024)
11-32830614-A-G		not specified	Uncertain significance (Jul 12, 2023)
11-32830626-G-A		PRRG4-related disorder	Benign (Nov 26, 2019)
11-32830640-C-T		PRRG4-related disorder	Benign (Nov 26, 2019)
11-32836676-A-C		not specified	Uncertain significance (Apr 23, 2024)
11-32836741-G-A		not specified	Uncertain significance (May 20, 2024)
11-32836772-T-C		not specified	Uncertain significance (Feb 15, 2023)
11-32840107-A-G		not specified	Uncertain significance (Mar 29, 2022)
11-32840156-T-G		not specified	Uncertain significance (Apr 06, 2024)
11-32840218-G-A		not specified	Uncertain significance (Jan 18, 2022)
11-32840223-A-G		not specified	Uncertain significance (Jul 14, 2023)
11-32853297-T-A		PRRG4-related disorder	Likely benign (Feb 04, 2021)
11-32853298-C-A		PRRG4-related disorder	Likely benign (Feb 04, 2021)
11-32853373-C-A		PRRG4-related disorder	Benign (Nov 26, 2019)
11-32853380-G-A		PRRG4-related disorder	Benign (Oct 18, 2019)
11-32853396-G-A		not specified	Likely benign (Mar 22, 2023)
11-32853507-A-G		not specified	Uncertain significance (Jun 07, 2023)
11-32853508-T-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRG4	protein_coding	protein_coding	ENST00000257836	5	28181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.113	0.862	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	78	118	0.660	0.00000574	1439
Missense in Polyphen		15	33.251	0.45112		431
Synonymous	0.933	37	45.0	0.823	0.00000223	454
Loss of Function	1.92	3	9.34	0.321	3.88e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000547	0.0000544
South Asian	0.000100	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May control axon guidance across the CNS (PubMed:28859078). Prevents the delivery of ROBO1 at the cell surface and downregulates its expression (PubMed:28859078). {ECO:0000269|PubMed:28859078}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.0784

Intolerance Scores

• loftool: 0.216
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.8

Haploinsufficiency Scores

• pHI: 0.0519
• hipred: N
• hipred_score: 0.233

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0549

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrg4

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular region;integral component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: molecular_function;calcium ion binding