PRRG1

proline rich and Gla domain 1, the group of Proline rich and Gla domain containing

Basic information

Region (hg38): X:37349309-37492702

Links

ENSG00000130962 ∙ NCBI:5638 ∙ OMIM:300935 ∙ HGNC:9469 ∙ Uniprot:O14668 ∙ 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 PRRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRG1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in PRRG1

This is a list of pathogenic ClinVar variants found in the PRRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-37425869-A-G		not specified	Likely benign (Mar 07, 2024)
X-37425894-A-G		not specified	Uncertain significance (Aug 19, 2024)
X-37425920-G-A		not specified	Uncertain significance (Nov 25, 2024)
X-37453184-C-G		not specified	Uncertain significance (Nov 27, 2023)
X-37453219-T-G		not specified	Uncertain significance (Dec 16, 2023)
X-37453241-A-G		not specified	Uncertain significance (Feb 27, 2024)
X-37453314-A-G		not specified	Uncertain significance (Dec 21, 2023)
X-37453318-C-T			Likely benign (Jan 01, 2023)
X-37453341-T-C		not specified	Uncertain significance (Oct 24, 2024)
X-37453344-A-C		not specified	Uncertain significance (Jun 05, 2024)
X-37453353-C-T		not specified	Uncertain significance (Jun 27, 2022)
X-37453362-C-G		not specified	Uncertain significance (Jan 07, 2022)
X-37453364-C-A		not specified	Uncertain significance (Jan 29, 2025)
X-37453401-C-T		not specified	Uncertain significance (Jun 07, 2023)
X-37453428-G-A		not specified	Uncertain significance (Jul 02, 2024)
X-37453449-G-A		not specified	Uncertain significance (Jun 17, 2024)
X-37453537-C-A		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRG1	protein_coding	protein_coding	ENST00000542554	3	108021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.131	0.788	125734	3	5	125742	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.409	71	81.4	0.873	0.00000628	1437
Missense in Polyphen		14	21.634	0.64714		431
Synonymous	-0.596	34	29.9	1.14	0.00000226	421
Loss of Function	1.40	2	5.58	0.358	4.22e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000113	0.0000981
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000626	0.0000462
European (Non-Finnish)	0.0000625	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.238
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.248
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrg1

Gene ontology

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