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. 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						0
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	1	0

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