ORMDL1

ORMDL sphingolipid biosynthesis regulator 1

Basic information

Region (hg38): 2:189766012-189784364

Links

ENSG00000128699 ∙ NCBI:94101 ∙ OMIM:610073 ∙ HGNC:16036 ∙ Uniprot:Q9P0S3 ∙ 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 ORMDL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ORMDL1 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	4	5
Total	0	0	8	1	4

Variants in ORMDL1

This is a list of pathogenic ClinVar variants found in the ORMDL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-189771792-C-T		not specified	Uncertain significance (Nov 18, 2023)
2-189771793-G-A		not specified	Uncertain significance (Feb 05, 2024)
2-189775575-G-C		not specified	Uncertain significance (Nov 13, 2024)
2-189775581-T-C		not specified	Uncertain significance (Oct 03, 2024)
2-189775591-C-A		not specified	Uncertain significance (Nov 24, 2024)
2-189775596-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-189775707-C-T		not specified	Uncertain significance (Sep 27, 2024)
2-189775712-A-G		not specified	Uncertain significance (Nov 08, 2022)
2-189782423-A-G		not specified	Uncertain significance (Jul 13, 2022)
2-189782435-A-G		not specified	Uncertain significance (Jun 27, 2022)
2-189782478-T-C		not specified	Uncertain significance (Nov 12, 2024)
2-189782508-C-T		not specified	Uncertain significance (Oct 14, 2021)
2-189783950-A-G			Benign (Apr 01, 2020)
2-189783978-G-C			Benign (Jul 20, 2018)
2-189783989-C-A			Benign (Apr 05, 2019)
2-189784079-G-T		Lynch syndrome	Benign/Likely benign (Jun 23, 2018)
2-189784312-C-T			Benign (Mar 03, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ORMDL1	protein_coding	protein_coding	ENST00000325795	3	14049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.123	0.788	125649	0	98	125747	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.777	66	86.3	0.765	0.00000467	998
Missense in Polyphen		34	45.849	0.74157		556
Synonymous	0.597	25	29.1	0.859	0.00000145	305
Loss of Function	1.36	2	5.41	0.370	2.29e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00278	0.00278
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.00	0.00
South Asian	0.000234	0.000229
Other	0.000825	0.000815

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: 0.113

Intolerance Scores

• loftool: 0.459
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.438
• hipred: Y
• hipred_score: 0.517
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ormdl1

Gene ontology

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