DEGS2

delta 4-desaturase, sphingolipid 2, the group of Fatty acid desaturases

Basic information

Region (hg38): 14:100143956-100159645

Previous symbols: [ "C14orf66" ]

Links

ENSG00000168350 ∙ NCBI:123099 ∙ OMIM:610862 ∙ HGNC:20113 ∙ Uniprot:Q6QHC5 ∙ 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 DEGS2 gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEGS2 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	2

Variants in DEGS2

This is a list of pathogenic ClinVar variants found in the DEGS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-100146860-G-A			Benign (Jul 29, 2018)
14-100146870-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-100146895-C-T		not specified	Uncertain significance (May 31, 2023)
14-100148977-G-C		not specified	Uncertain significance (Dec 08, 2023)
14-100149114-C-T		not specified	Uncertain significance (Mar 08, 2024)
14-100149224-G-A		not specified	Uncertain significance (Nov 09, 2021)
14-100149331-G-A			Benign (Apr 06, 2018)
14-100149356-G-A		not specified	Uncertain significance (Apr 20, 2023)
14-100149369-C-T		not specified	Uncertain significance (Jun 24, 2022)
14-100149378-C-T		not specified	Uncertain significance (Mar 29, 2023)
14-100149447-C-T		not specified	Uncertain significance (Oct 13, 2023)
14-100149483-G-A		not specified	Uncertain significance (Nov 08, 2022)
14-100149491-C-T		not specified	Uncertain significance (Jan 10, 2023)
14-100149495-C-T		not specified	Uncertain significance (Jul 12, 2022)
14-100149510-C-T		not specified	Likely benign (Jul 14, 2022)
14-100149539-G-A		not specified	Uncertain significance (Dec 14, 2023)
14-100149636-C-G		not specified	Uncertain significance (Apr 07, 2022)
14-100149669-G-A		not specified	Uncertain significance (Oct 03, 2022)
14-100149671-G-A		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEGS2	protein_coding	protein_coding	ENST00000305631	3	13745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000241	0.776	125670	0	10	125680	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	159	211	0.753	0.0000145	2037
Missense in Polyphen		64	92.187	0.69424		1007
Synonymous	-0.296	109	105	1.04	0.00000814	681
Loss of Function	1.08	7	10.8	0.647	4.66e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000933	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000566	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000561	0.0000528
Middle Eastern	0.0000566	0.0000544
South Asian	0.0000353	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bifunctional enzyme which acts as both a sphingolipid delta(4)-desaturase and a sphingolipid C4-monooxygenase. {ECO:0000269|PubMed:15063729}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Metabolism of lipids;Metabolism;ceramide <i>de novo</i> biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.531
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.0787
• hipred: Y
• hipred_score: 0.609
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.753

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Degs2

Gene ontology

• Biological process: sphinganine metabolic process;sphingolipid biosynthetic process;ceramide biosynthetic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: sphingosine hydroxylase activity;sphingolipid delta-4 desaturase activity