PRRG2

proline rich and Gla domain 2, the group of Proline rich and Gla domain containing

Basic information

Region (hg38): 19:49580646-49591004

Links

ENSG00000126460 ∙ NCBI:5639 ∙ OMIM:604429 ∙ HGNC:9470 ∙ Uniprot:O14669 ∙ 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 PRRG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRG2 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						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in PRRG2

This is a list of pathogenic ClinVar variants found in the PRRG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49583553-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-49583556-C-T		not specified	Likely benign (Jan 26, 2023)
19-49583557-C-G		not specified	Uncertain significance (Apr 17, 2023)
19-49583605-C-A		not specified	Uncertain significance (Jan 23, 2024)
19-49583620-T-C		not specified	Uncertain significance (Oct 26, 2022)
19-49583685-G-A		not specified	Uncertain significance (Feb 10, 2022)
19-49583715-A-G		not specified	Uncertain significance (Mar 29, 2024)
19-49583917-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-49588497-G-A		not specified	Uncertain significance (Jan 08, 2025)
19-49588520-A-T		not specified	Uncertain significance (Oct 26, 2022)
19-49588545-G-T		not specified	Uncertain significance (Jun 11, 2024)
19-49588568-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-49588568-G-T		not specified	Uncertain significance (Oct 02, 2023)
19-49588572-T-A		not specified	Uncertain significance (Jul 02, 2024)
19-49588593-G-A		not specified	Likely benign (Oct 26, 2022)
19-49588599-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-49589937-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-49589940-G-C		not specified	Uncertain significance (Sep 06, 2022)
19-49589953-C-G		not specified	Uncertain significance (Jun 04, 2024)
19-49589964-C-A		not specified	Uncertain significance (Jan 19, 2024)
19-49590039-C-T		not specified	Uncertain significance (May 29, 2024)
19-49590042-C-G		not specified	Uncertain significance (Aug 17, 2021)
19-49590042-C-T		not specified	Uncertain significance (Jun 13, 2023)
19-49590043-C-T		not specified	Uncertain significance (May 20, 2024)
19-49590372-C-T		not specified	Uncertain significance (Jan 16, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRG2	protein_coding	protein_coding	ENST00000246794	6	10370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.06e-7	0.325	125559	0	189	125748	0.000752

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0886	110	107	1.02	0.00000565	1252
Missense in Polyphen		40	40.111	0.99722		469
Synonymous	-0.454	46	42.2	1.09	0.00000183	432
Loss of Function	0.396	10	11.4	0.874	7.05e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00915	0.00919
Ashkenazi Jewish	0.00	0.00
East Asian	0.000431	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.000431	0.000381
South Asian	0.0000327	0.0000327
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.406
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.35

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.170
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.536

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrg2
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: extracellular region;integral component of plasma membrane
• Molecular function: calcium ion binding;protein binding