P3H4

prolyl 3-hydroxylase family member 4 (inactive), the group of Prolyl 3-hydroxylase family

Basic information

Region (hg38): 17:41801947-41812604

Previous symbols: [ "LEPREL4" ]

Links

ENSG00000141696 ∙ NCBI:10609 ∙ OMIM:617419 ∙ HGNC:16946 ∙ Uniprot:Q92791 ∙ 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 P3H4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P3H4 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				2		2
missense			45	1		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	0

Variants in P3H4

This is a list of pathogenic ClinVar variants found in the P3H4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-41802962-C-G		not specified	Uncertain significance (Jan 19, 2024)
17-41802962-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-41802970-G-A		not specified	Uncertain significance (Oct 17, 2023)
17-41803320-C-T		not specified	Uncertain significance (Aug 30, 2021)
17-41803350-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-41803406-G-A		not specified	Uncertain significance (Jan 29, 2024)
17-41803429-C-T		not specified	Uncertain significance (May 08, 2024)
17-41806801-C-G		not specified	Uncertain significance (Feb 08, 2025)
17-41806828-A-T		not specified	Uncertain significance (May 28, 2024)
17-41806842-C-T		not specified	Uncertain significance (Jun 19, 2024)
17-41806843-G-A		not specified	Uncertain significance (Nov 26, 2024)
17-41806854-G-T		not specified	Uncertain significance (Oct 11, 2024)
17-41807879-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-41807903-G-A		not specified	Uncertain significance (Jan 24, 2025)
17-41807939-C-T		not specified	Likely benign (Aug 02, 2021)
17-41807941-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-41807978-T-C		not specified	Uncertain significance (Dec 15, 2022)
17-41807980-C-T		not specified	Uncertain significance (May 03, 2023)
17-41807983-G-A		not specified	Uncertain significance (Jun 02, 2023)
17-41809745-C-T		not specified	Uncertain significance (Nov 30, 2022)
17-41809748-C-T		not specified	Uncertain significance (Mar 19, 2024)
17-41809757-C-G		not specified	Uncertain significance (May 08, 2023)
17-41809760-C-T		not specified	Uncertain significance (Jan 20, 2023)
17-41809781-G-C		not specified	Uncertain significance (Dec 25, 2024)
17-41810874-G-A		not specified	Uncertain significance (Feb 13, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P3H4	protein_coding	protein_coding	ENST00000355468	8	10658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.50e-10	0.203	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.498	235	258	0.913	0.0000149	2814
Missense in Polyphen		97	100.72	0.96305		1143
Synonymous	1.09	99	114	0.870	0.00000688	847
Loss of Function	0.678	17	20.3	0.838	8.66e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000407	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000296	0.000229
Other	0.000163	0.000163

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-linking of collagen fibrils. Required for normal bone density and normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly. {ECO:0000250|UniProtKB:Q8K2B0}.

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.309
• ghis: 0.532

Mouse Genome Informatics

• Gene name: P3h4
• Phenotype: muscle 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); skeleton phenotype

Gene ontology

• Biological process: synaptonemal complex assembly;peptidyl-lysine hydroxylation;collagen fibril organization;collagen biosynthetic process;bone remodeling
• Cellular component: condensed nuclear chromosome;synaptonemal complex;nucleolus;endoplasmic reticulum;catalytic complex