OMD

osteomodulin, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 9:92412380-92424471

Links

ENSG00000127083 ∙ NCBI:4958 ∙ OMIM:618926 ∙ HGNC:8134 ∙ Uniprot:Q99983 ∙ 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 OMD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OMD 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in OMD

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

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

Position	Type	Phenotype	Significance	ClinVar
9-92415190-C-T		not specified	Uncertain significance (Sep 22, 2023)
9-92415316-T-C		not specified	Uncertain significance (Mar 28, 2022)
9-92415321-C-T		not specified	Uncertain significance (Nov 27, 2023)
9-92415345-T-C		not specified	Uncertain significance (Jan 18, 2023)
9-92415346-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-92415350-A-T		not specified	Uncertain significance (Jan 03, 2022)
9-92415361-A-T		not specified	Uncertain significance (Feb 23, 2023)
9-92415411-C-T		not specified	Uncertain significance (Sep 01, 2021)
9-92416709-C-G		not specified	Uncertain significance (Nov 10, 2022)
9-92416715-T-C		not specified	Uncertain significance (Nov 07, 2023)
9-92416732-A-G		not specified	Uncertain significance (Sep 06, 2022)
9-92416780-T-C		not specified	Uncertain significance (May 15, 2024)
9-92416822-G-T		not specified	Uncertain significance (Aug 12, 2021)
9-92416840-A-G		not specified	Uncertain significance (Apr 25, 2023)
9-92416852-A-C		not specified	Uncertain significance (Jul 11, 2023)
9-92416957-G-A		not specified	Uncertain significance (Jun 07, 2023)
9-92416988-G-A		not specified	Uncertain significance (Dec 19, 2022)
9-92417164-A-G		not specified	Uncertain significance (Aug 08, 2023)
9-92417273-G-A		not specified	Uncertain significance (Nov 16, 2021)
9-92417290-G-A		not specified	Uncertain significance (Aug 04, 2021)
9-92417345-A-G		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OMD	protein_coding	protein_coding	ENST00000375550	2	10217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000124	0.622	125642	0	43	125685	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.756	184	215	0.855	0.0000101	2837
Missense in Polyphen		63	75.357	0.83602		1013
Synonymous	0.414	71	75.6	0.939	0.00000368	743
Loss of Function	0.872	9	12.3	0.732	6.14e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000386	0.000386
Ashkenazi Jewish	0.00	0.00
East Asian	0.000822	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000822	0.000816
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)- integrin (By similarity). {ECO:0000250}.
• Pathway: Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.597
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.0903
• hipred: N
• hipred_score: 0.167
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Omd
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;keratan sulfate biosynthetic process;regulation of bone mineralization;keratan sulfate catabolic process
• Cellular component: extracellular region;Golgi lumen;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome