PECR

peroxisomal trans-2-enoyl-CoA reductase, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 2:215996328-216082955

Links

ENSG00000115425 ∙ NCBI:55825 ∙ OMIM:605843 ∙ HGNC:18281 ∙ Uniprot:Q9BY49 ∙ 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 PECR gene.

• Inborn genetic diseases (18 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PECR 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			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	3

Variants in PECR

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

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

Position	Type	Phenotype	Significance	ClinVar
2-215996332-G-A		not specified	Uncertain significance (Jun 22, 2021)
2-215996349-T-C		not specified	Uncertain significance (Aug 02, 2023)
2-215996352-A-G		not specified	Uncertain significance (Feb 14, 2024)
2-215996377-T-C		not specified	Uncertain significance (Sep 16, 2021)
2-216013297-A-G		not specified	Uncertain significance (Jan 10, 2023)
2-216043907-G-A		not specified	Uncertain significance (Oct 19, 2021)
2-216043924-G-A		not specified	Uncertain significance (Jul 26, 2023)
2-216049289-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-216049300-T-C		not specified	Uncertain significance (Jan 26, 2023)
2-216049303-A-C		not specified	Uncertain significance (Jan 04, 2024)
2-216049372-C-T		not specified	Uncertain significance (Apr 08, 2022)
2-216051453-G-T		not specified	Uncertain significance (Oct 26, 2021)
2-216051469-G-A		not specified	Uncertain significance (Feb 27, 2023)
2-216051490-C-G		not specified	Uncertain significance (Jun 09, 2022)
2-216051513-T-C		not specified	Uncertain significance (Sep 15, 2021)
2-216058896-C-G			Benign (Jan 02, 2018)
2-216058938-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-216058974-A-C		not specified	Uncertain significance (Nov 10, 2022)
2-216065338-G-A		not specified	Uncertain significance (Jul 09, 2021)
2-216065360-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-216065368-C-T		not specified	Uncertain significance (Jan 26, 2022)
2-216065419-T-G		not specified	Uncertain significance (Oct 27, 2022)
2-216065431-T-C		not specified	Uncertain significance (Mar 04, 2024)
2-216065472-A-T		not specified	Uncertain significance (Feb 11, 2022)
2-216066394-A-G			Benign (Jun 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PECR	protein_coding	protein_coding	ENST00000265322	8	86627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.00e-8	0.361	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0474	164	166	0.990	0.00000871	1949
Missense in Polyphen		68	68.874	0.9873		767
Synonymous	-1.05	74	63.3	1.17	0.00000335	605
Loss of Function	0.705	13	16.0	0.810	8.96e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000566	0.000564
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in chain elongation of fatty acids. Has no 2,4-dienoyl-CoA reductase activity.
• Pathway: Peroxisome - Homo sapiens (human);Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Allograft Rejection;Fatty Acid Biosynthesis;Mitochondrial LC-Fatty Acid Beta-Oxidation;Liver steatosis AOP;Metabolism of lipids;Metabolism of proteins;Alpha-oxidation of phytanate;Saturated fatty acids beta-oxidation;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism;phytol degradation (Consensus)

Recessive Scores

• pRec: 0.0599

Intolerance Scores

• loftool: 0.457
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.0981
• hipred: N
• hipred_score: 0.169
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pecr

Gene ontology

• Biological process: fatty acid alpha-oxidation;protein targeting to peroxisome;fatty acid biosynthetic process;phytol metabolic process;oxidation-reduction process
• Cellular component: mitochondrion;peroxisome;peroxisomal membrane;cytosol
• Molecular function: signaling receptor binding;2,4-dienoyl-CoA reductase (NADPH) activity;trans-2-enoyl-CoA reductase (NADPH) activity