P4HA2

prolyl 4-hydroxylase subunit alpha 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:132190147-132295315

Links

ENSG00000072682 ∙ NCBI:8974 ∙ OMIM:600608 ∙ HGNC:8547 ∙ Uniprot:O15460 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopia 25, autosomal dominant (Limited), mode of inheritance: AD
• myopia 25, autosomal dominant (Limited), mode of inheritance: Unknown
• myopia (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopia 25, autosomal dominant	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	25741866

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the P4HA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P4HA2 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	7		8
missense			52	2	1	55
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1	1		2
Total	0	0	56	10	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P4HA2	protein_coding	protein_coding	ENST00000401867	14	103478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000197	1.00	125554	0	194	125748	0.000772

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.821	272	313	0.869	0.0000182	3479
Missense in Polyphen		135	145.02	0.9309		1579
Synonymous	-0.0166	123	123	1.00	0.00000726	1045
Loss of Function	3.20	16	37.0	0.433	0.00000223	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00457	0.00458
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000739	0.000739
Middle Eastern	0.000272	0.000272
South Asian	0.000360	0.000359
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the post-translational formation of 4- hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins.
• Disease: DISEASE: Myopia 25, autosomal dominant (MYP25) [MIM:617238]: A refractive error of the eye, in which parallel rays from a distant object come to focus in front of the retina, vision being better for near objects than for far. {ECO:0000269|PubMed:25741866}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Amino Acid metabolism;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism (Consensus)

Recessive Scores

• pRec: 0.193

Intolerance Scores

• loftool: 0.956
• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• pHI: 0.308
• hipred: Y
• hipred_score: 0.542
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: P4ha2

Gene ontology

• Biological process: peptidyl-proline hydroxylation to 4-hydroxy-L-proline;electron transport chain
• Cellular component: nucleoplasm;endoplasmic reticulum;endoplasmic reticulum lumen;cytosol;intracellular membrane-bounded organelle
• Molecular function: procollagen-proline 4-dioxygenase activity;iron ion binding;electron transfer activity;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;L-ascorbic acid binding