P3H3

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

Basic information

Region (hg38): 12:6828406-6839847

Previous symbols: [ "LEPREL2" ]

Links

ENSG00000110811 ∙ NCBI:10536 ∙ OMIM:610342 ∙ HGNC:19318 ∙ Uniprot:Q8IVL6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (13 variants)
• not provided (2 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	13	1	0

Variants in P3H3

This is a list of pathogenic ClinVar variants found in the P3H3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-6828543-C-G		not specified	Uncertain significance (Jan 31, 2024)
12-6828553-A-C		not specified	Uncertain significance (Jul 09, 2021)
12-6828598-G-C		not specified	Uncertain significance (Apr 24, 2023)
12-6828636-A-C		not specified	Uncertain significance (Jan 10, 2023)
12-6828736-C-A		not specified	Uncertain significance (Sep 27, 2022)
12-6828807-G-T		not specified	Uncertain significance (Aug 28, 2023)
12-6828860-G-G			Benign (Dec 31, 2019)
12-6830429-T-G		not specified	Uncertain significance (Jun 27, 2023)
12-6830494-G-A		not specified	Likely benign (Feb 28, 2024)
12-6830533-G-C		not specified	Uncertain significance (Aug 17, 2022)
12-6830757-G-A			Likely benign (Jul 01, 2022)
12-6831269-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-6831280-G-C		not specified	Uncertain significance (Mar 08, 2024)
12-6833798-C-T		not specified	Uncertain significance (Jun 09, 2022)
12-6833808-G-T		not specified	Uncertain significance (Feb 10, 2022)
12-6834018-C-T		not specified	Uncertain significance (Jan 04, 2022)
12-6837000-G-A		not specified	Uncertain significance (Mar 24, 2023)
12-6837958-C-T			Likely benign (Jul 01, 2022)
12-6837989-G-A		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P3H3	polymorphic_pseudogene	protein_coding	ENST00000396725	16	11447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.11e-12	0.642	124545	1	113	124659	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0383	363	361	1.01	0.0000230	4568
Missense in Polyphen		162	148.17	1.0934		1807
Synonymous	0.167	137	140	0.982	0.00000811	1564
Loss of Function	1.51	22	31.1	0.707	0.00000149	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000995	0.000991
Ashkenazi Jewish	0.000502	0.000497
East Asian	0.000511	0.000501
Finnish	0.000203	0.000186
European (Non-Finnish)	0.000300	0.000292
Middle Eastern	0.000511	0.000501
South Asian	0.00116	0.00114
Other	0.000167	0.000165

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

• 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