ORMDL2

ORMDL sphingolipid biosynthesis regulator 2

Basic information

Region (hg38): 12:55818041-55821879

Links

ENSG00000123353 ∙ NCBI:29095 ∙ OMIM:610074 ∙ HGNC:16037 ∙ Uniprot:Q53FV1 ∙ 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 ORMDL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ORMDL2 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			13	1	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	1

Variants in ORMDL2

This is a list of pathogenic ClinVar variants found in the ORMDL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-55819038-C-A		not specified	Uncertain significance (Jun 22, 2021)
12-55819076-A-C		not specified	Uncertain significance (Oct 12, 2024)
12-55819100-A-G		not specified	Uncertain significance (Sep 28, 2022)
12-55819102-A-G		not specified	Likely benign (Dec 21, 2022)
12-55819104-G-A		not specified	Uncertain significance (Apr 13, 2023)
12-55819115-G-A		not specified	Uncertain significance (Dec 02, 2024)
12-55819156-A-C			Benign (Dec 31, 2019)
12-55819364-C-T		not specified	Uncertain significance (Dec 21, 2023)
12-55819388-C-A		not specified	Uncertain significance (Jul 16, 2024)
12-55819463-G-A		not specified	Uncertain significance (Dec 07, 2021)
12-55819481-C-G		not specified	Uncertain significance (Oct 05, 2022)
12-55820288-T-G		not specified	Uncertain significance (Nov 06, 2024)
12-55820298-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-55820369-C-T		not specified	Uncertain significance (Jun 16, 2023)
12-55820370-G-A		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ORMDL2	protein_coding	protein_coding	ENST00000243045	3	3961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.194	0.763	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	78	90.3	0.863	0.00000499	992
Missense in Polyphen		21	24.894	0.84357		307
Synonymous	0.185	36	37.4	0.962	0.00000214	313
Loss of Function	1.68	2	6.71	0.298	4.56e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000289
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of sphingolipid synthesis. {ECO:0000269|PubMed:20182505}.
• Pathway: Metabolism of lipids;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0790

Intolerance Scores

• loftool: 0.240
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.328
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.545

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ormdl2

Gene ontology

• Biological process: ceramide metabolic process;cellular sphingolipid homeostasis;negative regulation of ceramide biosynthetic process
• Cellular component: endoplasmic reticulum;integral component of membrane;SPOTS complex