P3H2 prolyl 3-hydroxylase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: P3H2provided by HGNC
Official Full Name: prolyl 3-hydroxylase 2provided by HGNC
Primary source: HGNC:HGNC:19317
See related: Ensembl:ENSG00000090530 MIM:610341; AllianceGenome:HGNC:19317
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MCVD; MLAT4; LEPREL1
Summary: This gene encodes a member of the prolyl 3-hydroxylase subfamily of 2-oxo-glutarate-dependent dioxygenases. These enzymes play a critical role in collagen chain assembly, stability and cross-linking by catalyzing post-translational 3-hydroxylation of proline residues. Mutations in this gene are associated with nonsyndromic severe myopia with cataract and vitreoretinal degeneration, and downregulation of this gene may play a role in breast cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression: Broad expression in prostate (RPKM 22.0), kidney (RPKM 21.3) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q28

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (189956728..190122278, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (192773118..192938644, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (189674517..189840067, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis.
Title: Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis.
Mutation in the LEPREL1 gene is associated with ectopia lentis.
Title: Further phenotypic characterization of LEPREL1-related ectopia lentis.
Data identified an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk.
Title: Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk.
Recessive LEPREL1 mutations should be recognized as part of the differential diagnosis of lens subluxation.
Title: Recessive mutations in LEPREL1 underlie a recognizable lens subluxation phenotype.
LEPREL1 plays an important role in eye development and homozygous loss-of-function mutation of this gene can cause severely high myopia and early-onset cataract.
Title: Homozygous loss-of-function mutation of the LEPREL1 gene causes severe non-syndromic high myopia with early-onset cataract.
mutation in LRPAP1 is associated with high myopia. Further studies are expected to evaluate the pathogenicity of the variants in CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2.
Title: Detection of mutations in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 in 298 families with early-onset high myopia by exome sequencing.
High myopia is caused by a mutation in LEPREL1, encoding prolyl 3-hydroxylase 2.
Title: High myopia caused by a mutation in LEPREL1, encoding prolyl 3-hydroxylase 2.
P3H2 has preferred substrate sequences among the classes of 3Hyp sites in clade A collagen chains
Title: A role for prolyl 3-hydroxylase 2 in post-translational modification of fibril-forming collagens.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Myopia, high, with cataract and vitreoretinal degeneration MedGen: C3280346 OMIM: 614292 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S2379 (e-PCR)
- UniSTS:45103

STS-N21495 (e-PCR)
- UniSTS:21296

SHGC-82105 (e-PCR)
- UniSTS:103031

RH93767 (e-PCR)
- UniSTS:87517

D3S1661 (e-PCR)
- UniSTS:38894

RH65174 (e-PCR)
- UniSTS:86514

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-ascorbic acid binding	IEA Inferred from Electronic Annotation more info
enables iron ion binding	IEA Inferred from Electronic Annotation more info
enables procollagen-proline 3-dioxygenase activity	IBA Inferred from Biological aspect of Ancestor more info
enables procollagen-proline 3-dioxygenase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in collagen metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-proline hydroxylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IDA Inferred from Direct Assay more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in sarcoplasmic reticulum	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: prolyl 3-hydroxylase 2

Names: leprecan-like 1; myxoid liposarcoma-associated protein 4; procollagen-proline 3-dioxygenase 2; prolyl 3-hydroxylase 3

NP_001127890.1

EC 1.14.11.7

NP_060662.2

EC 1.14.11.7

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_031929.1 RefSeqGene

Range

6541..170710

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001134418.2 → NP_001127890.1 prolyl 3-hydroxylase 2 isoform b

See identical proteins and their annotated locations for NP_001127890.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.

Source sequence(s)

AC016966, BC005029, BU621129, BU737886, DA720646

Consensus CDS

CCDS46981.1

UniProtKB/Swiss-Prot

Q8IVL5

Related

ENSP00000408947.2, ENST00000427335.6

Conserved Domains (2) summary

smart00702
Location:291 → 489

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

cl21750
Location:130 → 163

Fis1; Mitochondrial Fission Protein Fis1, cytosolic domain
NM_018192.4 → NP_060662.2 prolyl 3-hydroxylase 2 isoform a precursor

See identical proteins and their annotated locations for NP_060662.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AJ430351, AK125134, BC005029, BU621129, BU737886

Consensus CDS

CCDS3294.1

UniProtKB/Swiss-Prot

B3KPK0, B3KWI9, D3DNV8, Q8IVL5, Q9NVI2

Related

ENSP00000316881.5, ENST00000319332.10

Conserved Domains (2) summary

smart00702
Location:472 → 670

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

cl21750
Location:311 → 344

Fis1; Mitochondrial Fission Protein Fis1, cytosolic domain