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.

• not_specified (16 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000014182.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	1	1

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