OCM2

protein-coding

oncomodulin 2, the group of EF-hand domain containing

Gene summary

This gene is similar to the oncomodulin gene, a high-affinity calcium ion-binding protein that belongs to the superfamily of calmodulin proteins, also known as the EF-hand proteins. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006188.4

Inheritance

—

ClinVar variants

U:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr7:97,984,687-97,991,169

External References & Databases

Ensembl (ENSG00000135175)

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 OCM2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006188.4. 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						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	0	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006188.4	RefSeq	NP_006179.2	4	MANE Select
ENST00000257627.5	Ensembl	ENSP00000257627.4	4	MANE Select

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: ENST00000257627
Coding exons: 4
Length: 6486
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 75
Defined: 125745
p: 0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0279	64	64.6	0.990	0.00000367	733
Missense (PolyPhen)		20	22.526	0.88787		254
Synonymous	0.633	23	27.2	0.845	0.00000198	187
Loss of Function	0.986	3	5.50	0.546	2.32e-7	67

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0042	0.0042	notable
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.666
RVIS EVS: 0.41
RVIS percentile EVS: 76.67

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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