PYCR3

pyrroline-5-carboxylate reductase 3

Basic information

Region (hg38): 8:143603209-143609773

Previous symbols: [ "PYCRL" ]

Links

ENSG00000104524 ∙ NCBI:65263 ∙ OMIM:616408 ∙ HGNC:25846 ∙ Uniprot:Q53H96 ∙ 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 PYCR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYCR3 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			24	2		26
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in PYCR3

This is a list of pathogenic ClinVar variants found in the PYCR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143605709-G-C		not specified	Uncertain significance (Jun 29, 2023)
8-143605726-G-A		not specified	Uncertain significance (Jun 23, 2021)
8-143605731-G-A		not specified	Uncertain significance (Mar 06, 2023)
8-143605744-C-T		not specified	Uncertain significance (Jun 19, 2024)
8-143605747-C-T		not specified	Uncertain significance (Aug 28, 2023)
8-143605764-C-T		not specified	Uncertain significance (Apr 17, 2024)
8-143605767-A-G		not specified	Uncertain significance (Apr 15, 2024)
8-143605791-A-G		not specified	Uncertain significance (Feb 10, 2022)
8-143605851-T-G		not specified	Uncertain significance (Dec 03, 2021)
8-143606085-G-A		not specified	Uncertain significance (May 17, 2023)
8-143606508-C-T		not specified	Uncertain significance (Jun 24, 2022)
8-143606534-C-T		not specified	Likely benign (Apr 12, 2022)
8-143606546-T-G		not specified	Uncertain significance (Jul 13, 2022)
8-143606574-C-T		not specified	Uncertain significance (Jun 04, 2024)
8-143606597-C-T		not specified	Uncertain significance (Jul 09, 2021)
8-143606600-G-A		not specified	Uncertain significance (Jun 29, 2023)
8-143606639-T-C		not specified	Uncertain significance (Nov 18, 2022)
8-143606651-C-T		not specified	Uncertain significance (Jul 26, 2022)
8-143606667-T-C		not specified	Uncertain significance (Aug 26, 2022)
8-143606966-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-143607015-C-A		not specified	Uncertain significance (Sep 20, 2023)
8-143607018-C-A		not specified	Uncertain significance (Jun 11, 2021)
8-143607075-C-T		not specified	Uncertain significance (Mar 16, 2023)
8-143607120-G-A		not specified	Uncertain significance (Dec 12, 2023)
8-143608093-G-A		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYCR3	protein_coding	protein_coding	ENST00000220966	6	5861

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000234	0.518	125531	1	57	125589	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00535	172	172	0.999	0.0000105	1779
Missense in Polyphen		67	70.038	0.95662		697
Synonymous	-1.47	93	76.6	1.21	0.00000499	637
Loss of Function	0.605	8	10.1	0.794	5.29e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000212	0.000208
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000381
Finnish	0.0000981	0.0000924
European (Non-Finnish)	0.000278	0.000273
Middle Eastern	0.000385	0.000381
South Asian	0.000367	0.000327
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enzyme that catalyzes the last step in proline biosynthesis. Proline is synthesized from either glutamate or ornithine; both are converted to pyrroline-5-carboxylate (P5C), and then to proline via pyrroline-5-carboxylate reductases (PYCRs). PYCRL is exclusively linked to the conversion of ornithine to proline. {ECO:0000269|PubMed:23024808}.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Urea cycle and metabolism of amino groups;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;proline biosynthesis;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.0936
• hipred: Y
• hipred_score: 0.510
• ghis: 0.475

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pycrl

Zebrafish Information Network

• Gene name: pycr3
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: cellular amino acid biosynthetic process;oxidation-reduction process;L-proline biosynthetic process
• Cellular component: cytosol
• Molecular function: pyrroline-5-carboxylate reductase activity;protein binding