L3HYPDH

trans-L-3-hydroxyproline dehydratase

Basic information

Region (hg38): 14:59460363-59484408

Previous symbols: [ "C14orf149" ]

Links

ENSG00000126790 ∙ NCBI:112849 ∙ OMIM:614811 ∙ HGNC:20488 ∙ Uniprot:Q96EM0 ∙ 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 L3HYPDH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the L3HYPDH 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in L3HYPDH

This is a list of pathogenic ClinVar variants found in the L3HYPDH region.

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

Position	Type	Phenotype	Significance	ClinVar
14-59463767-G-T		not specified	Uncertain significance (Jul 05, 2023)
14-59463782-G-A		not specified	Uncertain significance (Apr 04, 2023)
14-59463819-A-G		not specified	Uncertain significance (Aug 17, 2021)
14-59463851-A-G		not specified	Uncertain significance (Jun 11, 2024)
14-59463909-C-T		not specified	Uncertain significance (May 03, 2023)
14-59463927-A-T		not specified	Uncertain significance (May 25, 2022)
14-59464049-T-C		not specified	Uncertain significance (Jun 07, 2024)
14-59464065-C-T		not specified	Uncertain significance (Apr 09, 2024)
14-59464071-T-C		not specified	Uncertain significance (Oct 25, 2022)
14-59464073-A-G		not specified	Uncertain significance (Nov 08, 2021)
14-59464110-C-T		not specified	Uncertain significance (Sep 22, 2022)
14-59464157-C-T		not specified	Uncertain significance (May 30, 2022)
14-59464191-G-C		not specified	Uncertain significance (Dec 15, 2023)
14-59464199-C-A		not specified	Uncertain significance (Sep 28, 2022)
14-59464215-C-T		not specified	Uncertain significance (Jan 20, 2023)
14-59464286-A-G		not specified	Uncertain significance (Jun 24, 2022)
14-59464287-C-T		not specified	Uncertain significance (May 13, 2022)
14-59464314-G-T		not specified	Uncertain significance (Jan 17, 2024)
14-59464320-T-A		not specified	Uncertain significance (Mar 14, 2024)
14-59464346-C-T		not specified	Uncertain significance (Apr 28, 2022)
14-59464428-A-G		not specified	Uncertain significance (Jan 23, 2024)
14-59464445-C-A		not specified	Uncertain significance (Oct 04, 2022)
14-59464485-C-G		not specified	Likely benign (Jan 23, 2024)
14-59464499-G-A		not specified	Uncertain significance (Mar 29, 2022)
14-59464529-G-A		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
L3HYPDH	protein_coding	protein_coding	ENST00000247194	5	24068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.26e-7	0.329	125658	1	87	125746	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.359	216	202	1.07	0.00000936	2237
Missense in Polyphen		89	86.481	1.0291		898
Synonymous	1.11	71	83.9	0.846	0.00000423	746
Loss of Function	0.404	10	11.5	0.871	5.74e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.000443	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000300	0.000290
Middle Eastern	0.000443	0.000435
South Asian	0.000560	0.000523
Other	0.000692	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the dehydration of trans-3-hydroxy-L-proline to Delta(1)-pyrroline-2-carboxylate (Pyr2C). May be required to degrade trans-3-hydroxy-L-proline from the diet and originating from the degradation of proteins such as collagen-IV that contain it. {ECO:0000269|PubMed:22528483}.
• Pathway: Arginine and proline metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.309
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: L3hypdh

Gene ontology

• Molecular function: hydro-lyase activity;proline racemase activity;trans-L-3-hydroxyproline dehydratase activity