PRRG3

protein-coding

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

Gene summary

This gene encodes a protein which contains a vitamin K-dependent carboxylation/gamma-carboxyglutamic domain. The encoded protein is a member of a family of vitamin K-dependent transmembrane proteins which contain a glutamate-rich extracellular domain. [provided by RefSeq, Aug 2011]

MANE transcript

NM_001372163.1

Inheritance

—

ClinVar variants

U:55B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chrX:151,694,607-151,705,924

External References & Databases

Ensembl (ENSG00000130032)

Transcript & Mutation Effects

hg38 • Region Span ~11.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRRG3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001372163.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			47 clinvar	2 clinvar		49
nonsense			4 clinvar			4
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	55	3	0	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001372163.1	RefSeq	NP_001359092.1	3	MANE Select
ENST00000674457.1	Ensembl	ENSP00000501544.1	3	MANE Select
NM_001372165.1	RefSeq	NP_001359094.1	2	Standard
NM_024082.4	RefSeq	NP_076987.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

calcium ion binding

Cellular Component

extracellular region
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370353
Coding exons: 3
Length: 10801
Individuals with no LoFs: 125716
Homozygous LoFs: 9
Heterozygous LoFs: 18
Defined: 125743
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.756	127	105	1.21	0.00000919	1479
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000073	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00015	0.00011	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.00022	0.00016	rare
South Asian	0.00022	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.365
RVIS EVS: 0.62
RVIS percentile EVS: 83.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.272

Gene Damage Prediction

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