PRRG3

proline rich and Gla domain 3, the group of Proline rich and Gla domain containing

Basic information

Region (hg38): X:151694607-151705924

Links

ENSG00000130032 ∙ NCBI:79057 ∙ OMIM:300685 ∙ HGNC:30798 ∙ Uniprot:Q9BZD7 ∙ 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 PRRG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRG3 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in PRRG3

This is a list of pathogenic ClinVar variants found in the PRRG3 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-151700044-G-A		not specified	Uncertain significance (Oct 12, 2024)
X-151700050-A-G		not specified	Uncertain significance (Dec 07, 2021)
X-151700053-A-G		not specified	Uncertain significance (Oct 09, 2024)
X-151700071-G-A		not specified	Uncertain significance (Oct 12, 2022)
X-151700089-G-A		not specified	Uncertain significance (Jun 30, 2023)
X-151700154-A-G		not specified	Uncertain significance (Dec 24, 2024)
X-151700551-G-T		not specified	Uncertain significance (May 14, 2024)
X-151700560-C-G		not specified	Uncertain significance (Jun 11, 2024)
X-151700561-A-G		not specified	Uncertain significance (Jul 05, 2024)
X-151700590-C-A		not specified	Uncertain significance (May 02, 2024)
X-151700623-G-T		not specified	Uncertain significance (Dec 12, 2024)
X-151700666-G-A		not specified	Uncertain significance (Oct 12, 2024)
X-151700692-C-T		not specified	Uncertain significance (Feb 11, 2025)
X-151700693-G-A		not specified	Uncertain significance (Mar 01, 2025)
X-151700707-C-T		not specified	Uncertain significance (Feb 28, 2025)
X-151700719-A-G		not specified	Uncertain significance (Oct 12, 2024)
X-151700722-C-G		not specified	Uncertain significance (Sep 17, 2021)
X-151700759-G-A		not specified	Uncertain significance (Oct 25, 2024)
X-151700777-G-A		not specified	Uncertain significance (Aug 26, 2024)
X-151700783-G-A		not specified	Uncertain significance (Jun 21, 2023)
X-151700824-C-T		not specified	Uncertain significance (Jul 27, 2024)
X-151700827-G-C		not specified	Uncertain significance (Jul 25, 2023)
X-151700828-G-A		not specified	Uncertain significance (May 24, 2023)
X-151700845-C-T		not specified	Conflicting classifications of pathogenicity (May 13, 2024)
X-151700853-G-C		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRG3	protein_coding	protein_coding	ENST00000370353	3	10801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.95e-7	0.170	125716	9	18	125743	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.756	127	105	1.21	0.00000919	1479
Missense in Polyphen		36	35.945	1.0015		514
Synonymous	-2.57	66	44.3	1.49	0.00000380	486
Loss of Function	-0.186	9	8.42	1.07	8.37e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000729	0.0000729
Ashkenazi Jewish	0.00	0.00
East Asian	0.000147	0.000109
Finnish	0.0000634	0.0000462
European (Non-Finnish)	0.000224	0.000158
Middle Eastern	0.000147	0.000109
South Asian	0.000217	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.365
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.277
• hipred: N
• hipred_score: 0.219
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.272

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrg3

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular region;integral component of membrane
• Molecular function: calcium ion binding