P3H3

prolyl 3-hydroxylase 3, the group of Prolyl 3-hydroxylase family

Basic information

Region (hg38): 12:6828407-6839847

Previous symbols: [ "LEPREL2" ]

Links

ENSG00000110811NCBI:10536OMIM:610342HGNC:19318Uniprot:Q8IVL6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the P3H3 gene.

  • not_specified (47 variants)
  • not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P3H3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014262.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
missense
43
clinvar
4
clinvar
47
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 43 7 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
P3H3polymorphic_pseudogeneprotein_codingENST00000396725 1611447
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.11e-120.64212454511131246590.000457
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.03833633611.010.00002304568
Missense in Polyphen162148.171.09341807
Synonymous0.1671371400.9820.000008111564
Loss of Function1.512231.10.7070.00000149383

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009950.000991
Ashkenazi Jewish0.0005020.000497
East Asian0.0005110.000501
Finnish0.0002030.000186
European (Non-Finnish)0.0003000.000292
Middle Eastern0.0005110.000501
South Asian0.001160.00114
Other0.0001670.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils. Required for normal hydroxylation of lysine residues in type I collagen chains in skin, bone, tendon, aorta and cornea. Required for normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly. Apparently not required for normal prolyl 3-hydroxylation on collagen chains, possibly because it functions redundantly with other prolyl 3-hydroxylases. {ECO:0000250|UniProtKB:Q8CG70}.;
Pathway
Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

pRec
0.305

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.170
ghis
0.501

Mouse Genome Informatics

Gene name
P3h3
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process
negative regulation of cell population proliferation;peptidyl-lysine hydroxylation;peptidyl-proline hydroxylation;collagen metabolic process;collagen biosynthetic process;oxidation-reduction process
Cellular component
endoplasmic reticulum;catalytic complex
Molecular function
iron ion binding;procollagen-proline 3-dioxygenase activity;L-ascorbic acid binding