ORM2

orosomucoid 2, the group of Lipocalins

Basic information

Region (hg38): 9:114329869-114333251

Links

ENSG00000228278 ∙ NCBI:5005 ∙ OMIM:138610 ∙ HGNC:8499 ∙ Uniprot:P19652 ∙ 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 ORM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ORM2 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				1	1	2
missense			12	4		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	5	1

Variants in ORM2

This is a list of pathogenic ClinVar variants found in the ORM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-114329909-C-T		not specified	Uncertain significance (Mar 01, 2023)
9-114329923-C-T			Likely benign (Mar 01, 2023)
9-114329953-G-A		not specified	Uncertain significance (Jun 27, 2023)
9-114329983-G-C		not specified	Uncertain significance (Nov 18, 2022)
9-114330004-G-A		not specified	Uncertain significance (Mar 07, 2023)
9-114330016-C-T		not specified	Likely benign (Aug 15, 2023)
9-114330475-C-G		not specified	Uncertain significance (Mar 15, 2024)
9-114330476-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-114330506-C-G		not specified	Uncertain significance (Feb 16, 2023)
9-114330516-T-A		not specified	Uncertain significance (Mar 15, 2024)
9-114330835-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-114331622-G-C		not specified	Likely benign (Jun 22, 2023)
9-114331627-T-C		not specified	Uncertain significance (May 26, 2024)
9-114331643-C-T			Likely benign (Mar 01, 2023)
9-114331869-C-T			Benign (Feb 25, 2018)
9-114331879-G-C		not specified	Uncertain significance (Nov 28, 2023)
9-114331882-T-G		not specified	Uncertain significance (May 25, 2022)
9-114331918-G-A		not specified	Uncertain significance (Apr 15, 2024)
9-114331927-A-C		not specified	Uncertain significance (Dec 06, 2022)
9-114333093-C-A		not specified	Uncertain significance (Jul 20, 2022)
9-114333099-G-A		not specified	Uncertain significance (Sep 26, 2022)
9-114333124-G-A		not specified	Likely benign (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ORM2	protein_coding	protein_coding	ENST00000431067	6	3384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000200	0.470	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.19	142	107	1.32	0.00000608	1292
Missense in Polyphen		47	32.11	1.4637		367
Synonymous	-2.44	68	46.8	1.45	0.00000306	360
Loss of Function	0.674	10	12.6	0.795	6.88e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000438	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as transport protein in the blood stream. Binds various hydrophobic ligands in the interior of its beta- barrel domain. Also binds synthetic drugs and influences their distribution and availability. Appears to function in modulating the activity of the immune system during the acute-phase reaction. {ECO:0000269|PubMed:21349832}.
• Pathway: Vitamin D Receptor Pathway;Neutrophil degranulation;Innate Immune System;Immune System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.874
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.330
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Orm3

Gene ontology

• Biological process: platelet degranulation;regulation of immune system process;acute-phase response;neutrophil degranulation;positive regulation of interleukin-1 secretion;positive regulation of interleukin-1 beta secretion;positive regulation of tumor necrosis factor secretion
• Cellular component: extracellular region;extracellular space;platelet alpha granule lumen;azurophil granule lumen;specific granule lumen;collagen-containing extracellular matrix;extracellular exosome;blood microparticle