ORMDL1

ORMDL sphingolipid biosynthesis regulator 1

Basic information

Region (hg38): 2:189766012-189784364

Links

ENSG00000128699NCBI:94101OMIM:610073HGNC:16036Uniprot:Q9P0S3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
4
clinvar
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)3206980
2-189771793-G-A not specified Uncertain significance (Feb 05, 2024)3206979
2-189775575-G-C not specified Uncertain significance (Nov 13, 2024)3412419
2-189775581-T-C not specified Uncertain significance (Oct 03, 2024)3412416
2-189775591-C-A not specified Uncertain significance (Nov 24, 2024)2318668
2-189775596-G-A not specified Uncertain significance (Jan 16, 2024)3206978
2-189775707-C-T not specified Uncertain significance (Sep 27, 2024)3412415
2-189775712-A-G not specified Uncertain significance (Nov 08, 2022)2402220
2-189782423-A-G not specified Uncertain significance (Jul 13, 2022)2301461
2-189782435-A-G not specified Uncertain significance (Jun 27, 2022)2298071
2-189782478-T-C not specified Uncertain significance (Nov 12, 2024)3412417
2-189782508-C-T not specified Uncertain significance (Oct 14, 2021)2255449
2-189783950-A-G Benign (Apr 01, 2020)1253116
2-189783978-G-C Benign (Jul 20, 2018)1248274
2-189783989-C-A Benign (Apr 05, 2019)1292649
2-189784079-G-T Lynch syndrome Benign/Likely benign (Jun 23, 2018)369322
2-189784312-C-T Benign (Mar 03, 2015)1292217

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ORMDL1protein_codingprotein_codingENST00000325795 314049
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1230.7881256490981257470.000390
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7776686.30.7650.00000467998
Missense in Polyphen3445.8490.74157556
Synonymous0.5972529.10.8590.00000145305
Loss of Function1.3625.410.3702.29e-767

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002890.000275
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.002780.00278
European (Non-Finnish)0.0001870.000185
Middle Eastern0.000.00
South Asian0.0002340.000229
Other0.0008250.000815

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ormdl1
Phenotype

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
Molecular function