OCM

protein-coding

oncomodulin, the group of EF-hand domain containing

Gene summary

Oncomodulin is a high-affinity calcium ion-binding protein. It belongs to the superfamily of calmodulin proteins, also known as the EF-hand proteins. Oncomodulin is an oncodevelopmental protein found in early embryonic cells in the placenta and also in tumors. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001097622.2

Inheritance

—

ClinVar variants

U:23B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.62

Max pathogenic AF

—

Genomic locus

chr7:5,879,827-5,886,363

External References & Databases

Ensembl (ENSG00000122543)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OCM variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001097622.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			22 clinvar	1 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	1	0	24

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001097622.2	RefSeq	NP_001091091.1	4	MANE Select
ENST00000242104.6	Ensembl	ENSP00000242104.5	4	MANE Select
NM_001391990.1	RefSeq	NP_001378919.1	4	Standard
NM_001391991.1	RefSeq	NP_001378920.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of cytosolic calcium ion concentration

Molecular Function

calcium ion binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000242104
Coding exons: 4
Length: 6536
Individuals with no LoFs: 124898
Homozygous LoFs: 4
Heterozygous LoFs: 842
Defined: 125744
p: 0.00337

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.611	79	65.1	1.21	0.00000372	730
Missense (PolyPhen)		27	23.268	1.1604		255
Synonymous	-1.66	37	26.2	1.41	0.00000185	187
Loss of Function	-1.42	10	6.19	1.62	3.47e-7	68

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00069	0.00069	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.0035	0.0034	notable
European (Non-Finnish)	0.0062	0.0062	notable
South Asian	0.00056	0.00056	rare
Other	0.0029	0.0029	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has some calmodulin-like activity with respect to enzyme activation and growth regulation. Binds two calcium ions.;

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.716
RVIS EVS: 0.44
RVIS percentile EVS: 77.57

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0766

Gene Damage Prediction

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