GeneBe

P3H2

prolyl 3-hydroxylase 2, the group of Prolyl 3-hydroxylase family

Basic information

Region (hg38): 3:189956728-190122437

Previous symbols: [ "LEPREL1" ]

Links

ENSG00000090530 ∙ NCBI:55214 ∙ OMIM:610341 ∙ HGNC:19317 ∙ Uniprot:Q8IVL5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • myopia, high, with cataract and vitreoretinal degeneration (Strong), mode of inheritance: AR
  • myopia, high, with cataract and vitreoretinal degeneration (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myopia, high, with cataract and vitreoretinal degenerationARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic21885030; 24172257; 25469533

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the P3H2 gene.

  • not_provided (623 variants)
  • Inborn_genetic_diseases (128 variants)
  • P3H2-related_disorder (17 variants)
  • Myopia,_high,_with_cataract_and_vitreoretinal_degeneration (14 variants)
  • Myopia (1 variants)
  • Rare_isolated_myopia (1 variants)
  • Retinitis_pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P3H2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018192.4. 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
4
clinvar
131
clinvar
7
clinvar
 142
missense
2
clinvar
301
clinvar
11
clinvar
6
clinvar
 320
nonsense
16
clinvar
5
clinvar
3
clinvar
 24
start loss
0
frameshift
18
clinvar
2
clinvar
2
clinvar
 22
splice donor/acceptor (+/-2bp)
9
clinvar
1
clinvar
 10
Total 34 18 311 142 13

Highest pathogenic variant AF is 0.00015986616

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
P3H2protein_codingprotein_codingENST00000319332 15165710
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.79e-210.013312560601421257480.000565
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2353893761.030.00002014529
Missense in Polyphen11098.8961.11231182
Synonymous-0.6431551451.070.000007921383
Loss of Function0.7713439.20.8670.00000227451

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008440.000840
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.0003240.000323
European (Non-Finnish)0.0008270.000827
Middle Eastern0.0001630.000163
South Asian0.0004610.000457
Other0.0006520.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Prolyl 3-hydroxylase that catalyzes the post- translational formation of 3-hydroxyproline on collagens (PubMed:18487197). Contributes to proline 3-hydroxylation of collagen COL4A1 and COL1A1 in tendons, the eye sclera and in the eye lens capsule (By similarity). Has high activity with the type IV collagen COL4A1, and lower activity with COL1A1 (PubMed:18487197). Catalyzes hydroxylation of the first Pro in Gly-Pro-Hyp sequences where Hyp is 4-hydroxyproline (PubMed:18487197). Has no activity on substrates that lack 4- hydroxyproline in the third position (PubMed:18487197). {ECO:0000250|UniProtKB:Q8CG71, ECO:0000269|PubMed:18487197}.;
Pathway
Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

pRec
0.132

Intolerance Scores

loftool
rvis_EVS
-0.55
rvis_percentile_EVS
19.8

Haploinsufficiency Scores

pHI
0.142
hipred
N
hipred_score
0.394
ghis
0.501

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
P3h2
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
negative regulation of cell population proliferation;peptidyl-proline hydroxylation;collagen metabolic process;oxidation-reduction process
Cellular component
basement membrane;endoplasmic reticulum;endoplasmic reticulum lumen;Golgi apparatus;sarcoplasmic reticulum
Molecular function
iron ion binding;procollagen-proline 3-dioxygenase activity;L-ascorbic acid binding