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PRRG3

gene
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Also known as TMG3

Summary

PRRG3 (proline rich and Gla domain 3, HGNC:30798) is a protein-coding gene on chromosome Xq28, encoding Transmembrane gamma-carboxyglutamic acid protein 3 (Q9BZD7).

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.

Source: NCBI Gene 79057 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 58 total
  • GTEx eGene: eQTL in 45 tissues, sQTL in 0 (q < 0.05)
  • MANE Select transcript: NM_001372163
  • Notable: 58 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30798
Approved symbolPRRG3
Nameproline rich and Gla domain 3
LocationXq28
Locus typegene with protein product
StatusApproved
AliasesTMG3
Ensembl geneENSG00000130032
Ensembl biotypeprotein_coding
OMIM300685
Entrez79057

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

MANE Select: ENST00000674457

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 3: 2, TSL 5: 2

ENST00000674457, ENST00000370353, ENST00000370354, ENST00000448324, ENST00000448726, ENST00000538575, ENST00000652529, ENST00000674374, ENST00000674441, ENST00000884468, ENST00000913985

RefSeq mRNA: 3 — MANE Select: NM_001372163 NM_001372163, NM_001372165, NM_024082

CCDS: CCDS14699, CCDS94688

Canonical transcript exons

ENST00000674457 — 4 exons

ExonStartEnd
ENSE00001310099151699996151700156
ENSE00001452454151698784151698821
ENSE00003898222151695458151695544
ENSE00004779773151700506151705924

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 97.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1202 / max 8.4983, expressed in 55 samples.

Highest expression (Bgee): sural nerve, primordial germ cell in gonad, trigeminal ganglion, prefrontal cortex, tibial nerve.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRRG3 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 45 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 45 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Thyroideqtl1.1e-128-0.79X:151695519:C:T
Skin Not Sun Exposed Suprapubiceqtl1.7e-67-0.40X:151694751:CG:C
Skin Sun Exposed Lower legeqtl7.3e-64-0.34X:151695519:C:T
Esophagus Mucosaeqtl6.3e-61-0.41X:151695519:C:T
Pituitaryeqtl7.0e-53-0.78X:151695519:C:T
Muscle Skeletaleqtl5.1e-42-0.30X:151694751:CG:C
Adipose Visceral Omentumeqtl4.3e-38-0.32X:151695519:C:T
Lungeqtl1.8e-34-0.36X:151695519:C:T
Testiseqtl4.7e-34-0.58X:151695519:C:T
Prostateeqtl5.3e-34-0.58X:151695519:C:T
Heart Atrial Appendageeqtl1.1e-33-0.43X:151695519:C:T
Adipose Subcutaneouseqtl7.8e-33-0.20X:151695519:C:T
Heart Left Ventricleeqtl4.7e-32-0.33X:151694751:CG:C
Colon Sigmoideqtl8.9e-30-0.34X:151695519:C:T
Esophagus Musculariseqtl5.4e-28-0.27X:151695519:C:T
Nerve Tibialeqtl5.7e-28+0.13X:151702241:C:G
Breast Mammary Tissueeqtl5.2e-27-0.24X:151695519:C:T
Brain Hypothalamuseqtl1.2e-20-0.22X:151695519:C:T
Brain Cerebellumeqtl1.6e-20-0.50X:151694751:CG:C
Colon Transverseeqtl1.1e-19-0.19X:151695519:C:T

FANTOM5 promoters

1 alternative TSS:

Promoter IDTPM avgSamples expressed
2098650.120255

Top tissues by expression

showing 100 of 250 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548897.24gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.31gold quality
trigeminal ganglionUBERON:000167583.69gold quality
prefrontal cortexUBERON:000045181.53gold quality
tibial nerveUBERON:000132381.34gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.62gold quality
superior frontal gyrusUBERON:000266180.41gold quality
Brodmann (1909) area 23UBERON:001355480.26gold quality
cortical plateUBERON:000534380.04gold quality
frontal cortexUBERON:000187079.83gold quality
dorsolateral prefrontal cortexUBERON:000983479.77gold quality
hypothalamusUBERON:000189879.72gold quality
neocortexUBERON:000195079.58gold quality
anterior cingulate cortexUBERON:000983579.32gold quality
Brodmann (1909) area 9UBERON:001354078.75gold quality
ganglionic eminenceUBERON:000402378.73gold quality
right frontal lobeUBERON:000281078.71gold quality
dorsal root ganglionUBERON:000004478.48gold quality
primary visual cortexUBERON:000243678.35gold quality
nucleus accumbensUBERON:000188278.30gold quality
cerebral cortexUBERON:000095678.26gold quality
middle temporal gyrusUBERON:000277178.05gold quality
entorhinal cortexUBERON:000272877.81gold quality
postcentral gyrusUBERON:000258176.41gold quality
temporal lobeUBERON:000187175.13gold quality
parietal lobeUBERON:000187274.84gold quality
forebrainUBERON:000189074.82gold quality
occipital lobeUBERON:000202174.45gold quality
skin of hipUBERON:000155474.27gold quality
lateral nuclear group of thalamusUBERON:000273674.06gold quality
amygdalaUBERON:000187673.97gold quality
ventricular zoneUBERON:000305373.96gold quality
Brodmann (1909) area 46UBERON:000648373.58gold quality
Ammon’s hornUBERON:000195473.09gold quality
caudate nucleusUBERON:000187372.65gold quality
endocervixUBERON:000045872.49gold quality
hindlimb stylopod muscleUBERON:000425272.44gold quality
ectocervixUBERON:001224972.06gold quality
putamenUBERON:000187471.91gold quality
brainUBERON:000095571.33gold quality
adrenal tissueUBERON:001830371.32gold quality
colonic epitheliumUBERON:000039770.77gold quality
uterine cervixUBERON:000000270.30gold quality
apex of heartUBERON:000209869.85gold quality
tendon of biceps brachiiUBERON:000818867.82gold quality
cerebellar vermisUBERON:000472067.65gold quality
tendonUBERON:000004367.22gold quality
superior vestibular nucleusUBERON:000722766.95gold quality
nasal cavity epitheliumUBERON:000538466.84gold quality
substantia nigraUBERON:000203866.79gold quality
calcaneal tendonUBERON:000370166.79gold quality
layer of synovial tissueUBERON:000761666.53silver quality
midbrainUBERON:000189166.07gold quality
gall bladderUBERON:000211065.88gold quality
epithelium of nasopharynxUBERON:000195165.12gold quality
epithelial cell of pancreasCL:000008364.78gold quality
vaginaUBERON:000099664.22gold quality
pigmented layer of retinaUBERON:000178264.16gold quality
subcutaneous adipose tissueUBERON:000219063.89gold quality
left ovaryUBERON:000211963.71gold quality
mucosa of stomachUBERON:000119963.63gold quality
thoracic mammary glandUBERON:000520063.57gold quality
smooth muscle tissueUBERON:000113563.52gold quality
corpus epididymisUBERON:000435963.45gold quality
parotid glandUBERON:000183163.39gold quality
mammary glandUBERON:000191163.30gold quality
ovaryUBERON:000099263.14gold quality
mammary ductUBERON:000176563.08silver quality
epithelium of mammary glandUBERON:000324462.96silver quality
muscle tissueUBERON:000238562.87gold quality
heart left ventricleUBERON:000208462.73gold quality
endothelial cellCL:000011562.62gold quality
skeletal muscle tissueUBERON:000113462.61gold quality
cardiac ventricleUBERON:000208262.61gold quality
right uterine tubeUBERON:000130262.58gold quality
right ovaryUBERON:000211862.48gold quality
esophagogastric junction muscularis propriaUBERON:003584162.19gold quality
vena cavaUBERON:000408762.04gold quality
upper leg skinUBERON:000426262.04gold quality
superficial temporal arteryUBERON:000161461.98gold quality
body of uterusUBERON:000985361.98gold quality
olfactory segment of nasal mucosaUBERON:000538661.89gold quality
ponsUBERON:000098861.66silver quality
mammalian vulvaUBERON:000099761.41gold quality
zone of skinUBERON:000001461.35gold quality
minor salivary glandUBERON:000183061.23gold quality
lower esophagus muscularis layerUBERON:003583361.08gold quality
lower esophagusUBERON:001347361.04gold quality
adipose tissueUBERON:000101361.01gold quality
saliva-secreting glandUBERON:000104460.98gold quality
dorsal plus ventral thalamusUBERON:000189760.98silver quality
skin of legUBERON:000151160.94gold quality
lateral globus pallidusUBERON:000247660.88gold quality
synovial jointUBERON:000221760.55gold quality
substantia nigra pars compactaUBERON:000196560.43silver quality
mouth mucosaUBERON:000372960.38gold quality
skin of abdomenUBERON:000141660.35gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450260.16gold quality
muscle of legUBERON:000138360.13gold quality
ileal mucosaUBERON:000033160.04gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.36
E-MTAB-6678no2.42

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 74 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPM
Postcentral gyrustissue33.7
Locus coeruleustissue22.6
Nucleus accumbenstissue20.3
Prefrontal cortextissue18.9
Cerebral cortextissue18.9
Motor cortextissue17.6
Insular cortextissue17.2
Hypothalamustissue16.8
Hippocampustissue16.5
Hippocampal formationtissue16.4
Entorhinal cortextissue16.4
Retrosplenial and cingulate cortextissue16.3
Somatosensory cortextissue16.3
Temporal cortextissue15.5
Retrosplenial cortextissue15.3
Occipital cortextissue14.9
Frontal cortextissue14.5
Spinal cordtissue13.4
Amygdalatissue12.1
Septumtissue12.1
Ponstissue12.0
Thalamustissue11.4
Midbraintissue9.8
Ventral forebraintissue9.8
Periaqueductal graytissue9.7
Substantia nigratissue9.0
Olfactory bulbtissue9.0
Basal gangliatissue8.9
Caudate putamentissue8.6
Superior colliculitissue8.0
Putamentissue7.8
Epididymistissue7.0
Choroid plexustissue6.5
Medulla oblongatatissue6.0
Cervixtissue4.5
Vaginatissue2.6
Ovarytissue2.5
Esophagustissue2.2
Skeletal muscletissue2.2
Adipose tissuetissue1.8
Tonguetissue1.8
Gallbladdertissue1.8
Spleentissue1.6
Corpus callosumtissue1.6
Endometrium 1tissue1.5
Pituitary glandtissue1.4
Skin 1tissue1.4
Smooth muscletissue1.3
Breasttissue1.1
Lungtissue1.1
Thymustissue1.1
Heart muscletissue0.9
Urinary bladdertissue0.9
Salivary glandtissue0.7
Placentatissue0.7
Retinatissue0.6
Colontissue0.6
Rectumtissue0.5
Fallopian tubetissue0.5
Cerebellumtissue0.4

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Olfactory area (34.2), Stria terminalis, bed nucleus (33.9), Olfactory tubercle (32.8), Precentral gyrus (31.2), Ventromedial nucleus (31.2).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PRRG3 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 37 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-12118100.0065.881270
HSA-MIR-1213699.9872.815713
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-96-5P99.9572.802140
HSA-MIR-335-3P99.9373.364958
HSA-MIR-1213399.9271.822006
HSA-MIR-1271-5P99.9171.991972
HSA-MIR-153-5P99.8973.866317
HSA-MIR-182-5P99.8774.032589
HSA-MIR-94499.8270.853042
HSA-MIR-5002-5P99.7670.841763
HSA-MIR-397599.6265.97697
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-186-3P99.5166.241685
HSA-MIR-4687-3P99.4866.41968
HSA-MIR-431899.3866.941505
HSA-MIR-397899.2468.392201
HSA-MIR-593-3P99.2267.281327
HSA-MIR-196A-3P99.1967.341204
HSA-MIR-6734-3P99.1566.271627
HSA-MIR-4695-5P99.0664.871151
HSA-MIR-6852-3P98.5467.601468
HSA-MIR-6792-3P98.4166.861359
HSA-MIR-4691-5P98.4166.771343
HSA-MIR-891A-3P98.0567.99970
HSA-MIR-444398.0266.251928
HSA-MIR-393697.6464.47732

Functional genomics

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000674457 — one region, missense o/e 1.25.

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosi:dkey-38k9.5ENSDARG00000079102
mus_musculusPrrg3ENSMUSG00000033361
rattus_norvegicusPrrg3ENSRNOG00000066176

Paralogs (3): PRRG1 (ENSG00000130962), PRRG4 (ENSG00000135378), OVCH2 (ENSG00000183378)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Pongo abeliiQ5RCB699.5%Diamond
Macaca mulattaQ2852096.0%Diamond
Bos taurusA7Z07094.0%Diamond
Oryctolagus cuniculusP9811883.1%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
PASD1protein-coding139135
VMA21protein-coding203547
MAGEA4-AS1ncRNA105373368
MAGEA4protein-coding4103
FATE1protein-coding89885
CNGA2protein-coding1260

Protein

Protein identifiers

Transmembrane gamma-carboxyglutamic acid protein 3 — Q9BZD7 (reviewed: Q9BZD7)

Alternative names: Proline-rich gamma-carboxyglutamic acid protein 3

All UniProt accessions (6): Q9BZD7, A0A494BZY9, A0A6I8PL69, A6NDZ7, C9J7E6, H7C0C2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed in brain, lung, kidney and heart.

Post-translational modifications. Gla residues are produced after subsequent post-translational modifications of glutamate by a vitamin K-dependent gamma-carboxylase.

RefSeq proteins (3): NP_001359092, NP_001359094, NP_076987 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000294GLA_domainDomain
IPR017857Coagulation_fac-like_Gla_domHomologous_superfamily
IPR035972GLA-like_dom_SFHomologous_superfamily
IPR050442Peptidase_S1_coag_factorsFamily

Pfam: PF00594

UniProt features (25 total): modified residue 13, topological domain 2, region of interest 2, propeptide 1, chain 1, disulfide bond 1, sequence variant 1, sequence conflict 1, transmembrane region 1, domain 1, compositionally biased region 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BZD7-F164.480.10

Human Protein Atlas

Protein class: Predicted membrane proteins, Predicted intracellular proteins, UniProt - Evidence at transcript level

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH uncertain

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (13)

TypePositions
4-carboxyglutamate25, 26, 33, 35, 38, 39, 44, 45, 48, 51, 54, 58, 22

Disulfide bonds (1)

TypePositions
Disulfide bond36–41

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 64 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_WOUND_HEALING, RYTTCCTG_ETS2_B, GOBP_HEMOSTASIS, MODULE_48, MODULE_95, GOBP_REGULATION_OF_BODY_FLUID_LEVELS, GOBP_PROTEOLYSIS, GOMF_PEPTIDASE_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, chrXq28, PILON_KLF1_TARGETS_UP, MODULE_163, P53_DN.V2_UP, LMTK3_TARGET_GENES

GO Biological Process (2): proteolysis (GO:0006508), blood coagulation (GO:0007596)

GO Molecular Function (2): serine-type endopeptidase activity (GO:0004252), calcium ion binding (GO:0005509)

GO Cellular Component (2): membrane (GO:0016020), extracellular region (GO:0005576)

GO top-level categories

8 GO namespaces:

CategoryTerms
cellular anatomical structure2
protein metabolic process1
hemostasis1
wound healing1
coagulation1
endopeptidase activity1
serine-type peptidase activity1
metal ion binding1

Protein interactions and networks

STRING

showing 15 of 274 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
PRRG3GGCXP38435490
PRRG3CCDC116Q8IYX3466
PRRG3SSX3Q99909456
PRRG3UCMAQ8WVF2443
PRRG3LRRC52Q8N7C0416
PRRG3RNASE10Q5GAN6385
PRRG3AGFG2O95081360
PRRG3LRRC23Q53EV4356
PRRG3MGPP08493352
PRRG3ZNF3P13683351
PRRG3RFX7Q2KHR2351
PRRG3KANK3Q6NY19347
PRRG3GALNT15Q8N3T1345
PRRG3B4GALT4O60513345
PRRG3TCF23Q7RTU1329

IntAct

Human interaction partners of PRRG3 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

1 partners by confidence:

PartnerInteraction typeMIscoreRecords
NEDD4association0.3502

BioGRID (9 interactions; top human partners by supporting records): NDFIP1 (Affinity Capture-MS; 3 records), NEDD4L (Affinity Capture-MS; 3 records), NEDD4 (Affinity Capture-MS; 2 records), RNF149 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for PRRG3: 58 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

58 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign2
Benign0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 26 predictions of 527):

Position(s)EffectΔscoreSites
X:151700114donor_gain1.0000
X:151700130donor_gain1.0000
X:151695545–151695546donor_loss0.99005
X:151698782–151698783acceptor_loss0.99006
X:151700131donor_gain0.9900
X:151700504–151700505acceptor_loss0.99005
X:151695546donor_loss0.9800
X:151698778acceptor_gain0.9800
X:151698822–151698823donor_loss0.98004
X:151698823acceptor_loss0.9800

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

CancerPrognosticp-value
Glioblastoma Multiforme (TCGA)unfavorable0.000143

Disease associations

OMIM: gene MIM:300685 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, affects cotreatment, decreases expression4
bisphenol Faffects cotreatment, decreases expression1
sodium arseniteincreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Vorinostatdecreases expression1
Benzo(a)pyrenedecreases methylation, affects methylation1
Dexamethasonedecreases expression, affects cotreatment1
Indomethacinaffects cotreatment, decreases expression1
Nickeldecreases expression1
Tobacco Smoke Pollutiondecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1
Antirheumatic Agentsincreases expression1
Acrylamidedecreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.