P4HA3

prolyl 4-hydroxylase subunit alpha 3

Basic information

Region (hg38): 11:74235800-74311640

Links

ENSG00000149380 ∙ NCBI:283208 ∙ OMIM:608987 ∙ HGNC:30135 ∙ Uniprot:Q7Z4N8 ∙ 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 P4HA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P4HA3 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						0
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	33	1	0

Variants in P4HA3

This is a list of pathogenic ClinVar variants found in the P4HA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74235947-A-G		not specified	Uncertain significance (Jan 17, 2024)
11-74239225-T-C		not specified	Uncertain significance (Feb 23, 2023)
11-74239239-A-C		not specified	Uncertain significance (Jun 28, 2023)
11-74246081-G-C		not specified	Uncertain significance (Dec 27, 2023)
11-74246161-A-G		not specified	Uncertain significance (Nov 09, 2021)
11-74251664-C-G		not specified	Uncertain significance (Apr 07, 2023)
11-74253493-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-74253499-C-T		not specified	Uncertain significance (Jan 27, 2022)
11-74267300-T-C		not specified	Uncertain significance (Oct 14, 2021)
11-74268168-G-C		not specified	Uncertain significance (Apr 19, 2023)
11-74268193-T-C		not specified	Likely benign (Mar 29, 2024)
11-74268196-C-G			Likely benign (Sep 01, 2022)
11-74269689-G-A		not specified	Uncertain significance (May 20, 2024)
11-74279434-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-74285811-A-G		not specified	Uncertain significance (Oct 25, 2023)
11-74285820-C-A		not specified	Uncertain significance (Oct 06, 2022)
11-74285856-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-74285870-A-C		not specified	Uncertain significance (Feb 22, 2023)
11-74285936-G-T		not specified	Uncertain significance (Aug 13, 2021)
11-74285948-T-C		not specified	Uncertain significance (Dec 15, 2023)
11-74285954-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-74285985-G-A		not specified	Uncertain significance (Jul 07, 2022)
11-74286253-C-G		not specified	Uncertain significance (Mar 16, 2024)
11-74286280-T-C		not specified	Uncertain significance (May 13, 2024)
11-74286283-G-A		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P4HA3	protein_coding	protein_coding	ENST00000331597	13	75857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.80e-10	0.888	125689	0	57	125746	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.527	268	293	0.913	0.0000153	3464
Missense in Polyphen		81	90.313	0.89688		1070
Synonymous	0.968	104	117	0.886	0.00000611	1108
Loss of Function	1.80	19	29.6	0.643	0.00000159	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000648	0.000648
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000761	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000761	0.000761
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the post-translational formation of 4- hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins. {ECO:0000269|PubMed:12874193, ECO:0000269|PubMed:14500733}.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Hyperornithinemia with gyrate atrophy (HOGA);Creatine deficiency, guanidinoacetate methyltransferase deficiency;L-arginine:glycine amidinotransferase deficiency;Hyperornithinemia-hyperammonemia-homocitrullinuria [HHH-syndrome];Guanidinoacetate Methyltransferase Deficiency (GAMT Deficiency);Prolinemia Type II;Prolidase Deficiency (PD);Arginine and Proline Metabolism;Hyperprolinemia Type I;Hyperprolinemia Type II;Ornithine Aminotransferase Deficiency (OAT Deficiency);Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency);Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.821
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.0625
• hipred: N
• hipred_score: 0.251
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: P4ha3

Gene ontology

• Biological process: peptidyl-proline hydroxylation to 4-hydroxy-L-proline;oxidation-reduction process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: procollagen-proline 4-dioxygenase activity;iron ion binding;protein binding;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;L-ascorbic acid binding