DECR1

2,4-dienoyl-CoA reductase 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 8:90001405-90053633

Previous symbols: [ "DECR" ]

Links

ENSG00000104325 ∙ NCBI:1666 ∙ OMIM:222745 ∙ HGNC:2753 ∙ Uniprot:Q16698 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• progressive encephalopathy with leukodystrophy due to DECR deficiency (Limited), mode of inheritance: Unknown
• progressive encephalopathy with leukodystrophy due to DECR deficiency (No Known Disease Relationship), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
2,4-dienoyl-CoA reductase deficiency	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic	2332510

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DECR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DECR1 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	4
missense			16	6		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	16	8	3

Variants in DECR1

This is a list of pathogenic ClinVar variants found in the DECR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-90001511-G-T		not specified	Uncertain significance (Mar 04, 2024)
8-90001545-G-T		not specified	Uncertain significance (Aug 28, 2023)
8-90001550-G-A		Progressive encephalopathy with leukodystrophy due to DECR deficiency • not specified	Uncertain significance (Mar 25, 2024)
8-90006245-C-T		DECR1-related disorder	Likely benign (Apr 06, 2024)
8-90017131-G-A		Progressive encephalopathy with leukodystrophy due to DECR deficiency • DECR1-related disorder	Likely benign (May 12, 2021)
8-90017221-G-A		not specified	Uncertain significance (Jun 30, 2024)
8-90017256-G-A		Progressive encephalopathy with leukodystrophy due to DECR deficiency	Uncertain significance (Apr 27, 2019)
8-90017312-C-T		DECR1-related disorder	Likely benign (Sep 25, 2019)
8-90018917-A-G		not specified	Uncertain significance (Nov 10, 2022)
8-90019121-T-C		Progressive encephalopathy with leukodystrophy due to DECR deficiency	Benign (Feb 22, 2020)
8-90019123-T-C		not specified	Uncertain significance (Aug 04, 2021)
8-90019124-G-A		not specified	Uncertain significance (Mar 28, 2022)
8-90019125-G-A		not specified	Uncertain significance (Sep 16, 2021)
8-90020909-A-G		not specified	Likely benign (Jun 01, 2023)
8-90020923-T-C		Progressive encephalopathy with leukodystrophy due to DECR deficiency	Benign (Apr 18, 2018)
8-90020942-T-C		not specified	Uncertain significance (Sep 16, 2021)
8-90021009-C-T		not specified	Uncertain significance (Nov 15, 2024)
8-90021014-G-A		not specified	Likely benign (Sep 22, 2022)
8-90036894-G-T		Progressive encephalopathy with leukodystrophy due to DECR deficiency • not specified	Uncertain significance (Mar 25, 2024)
8-90042781-C-T		Progressive encephalopathy with leukodystrophy due to DECR deficiency	Likely benign (Jul 13, 2018)
8-90044862-G-A		not specified	Uncertain significance (Sep 27, 2021)
8-90044901-G-A		not specified	Likely benign (Oct 27, 2023)
8-90044918-C-T		not specified	Uncertain significance (Nov 07, 2024)
8-90044942-G-A		not specified	Uncertain significance (Apr 13, 2022)
8-90044970-A-G		DECR1-related disorder	Likely benign (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DECR1	protein_coding	protein_coding	ENST00000220764	10	50688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.47e-14	0.00688	125626	0	120	125746	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0316	180	181	0.993	0.00000890	2175
Missense in Polyphen		69	76.171	0.90586		845
Synonymous	0.561	56	61.6	0.909	0.00000320	678
Loss of Function	-0.582	19	16.5	1.15	7.79e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000799	0.000793
Ashkenazi Jewish	0.00	0.00
East Asian	0.000391	0.000381
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000391	0.000381
South Asian	0.00173	0.00173
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxiliary enzyme of beta-oxidation. It participates in the metabolism of unsaturated fatty enoyl-CoA esters having double bonds in both even- and odd-numbered positions. Catalyzes the NADP-dependent reduction of 2,4-dienoyl-CoA to yield trans-3- enoyl-CoA.
• Pathway: Fatty Acid Beta Oxidation;Fatty Acid Biosynthesis;Liver steatosis AOP;ccr3 signaling in eosinophils;Metabolism of lipids;mitochondrial fatty acid beta-oxidation of unsaturated fatty acids;Mitochondrial Fatty Acid Beta-Oxidation;3-oxo-10R-octadecatrienoate beta-oxidation;Metabolism;Fatty acid metabolism;Omega-6 fatty acid metabolism;Di-unsaturated fatty acid beta-oxidation (Consensus)

Recessive Scores

• pRec: 0.936

Intolerance Scores

• loftool: 0.640
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.467
• hipred: Y
• hipred_score: 0.564
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Decr1
• Phenotype: liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: fatty acid beta-oxidation;protein homotetramerization;positive regulation of cold-induced thermogenesis
• Cellular component: nucleus;nucleoplasm;mitochondrion;mitochondrial matrix;cytosol
• Molecular function: 2,4-dienoyl-CoA reductase (NADPH) activity;oxidoreductase activity, acting on NAD(P)H;NADPH binding