CAMKMT

protein-coding

calmodulin-lysine N-methyltransferase, the group of 7BS protein lysine methyltransferases

Gene summary

This gene encodes a class I protein methyltransferase that acts in the formation of trimethyllysine in calmodulin. The protein contains a AdoMet-binding motif and may play a role in calcium-dependent signaling. [provided by RefSeq, Sep 2012]

Previous symbols:

C2orf34

MANE transcript

NM_024766.5

Inheritance

—

ClinVar variants

U:62B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr2:44,361,947-44,772,592

External References & Databases

Ensembl (ENSG00000143919)

Transcript & Mutation Effects

hg38 • Region Span ~410.6 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 CAMKMT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024766.5. 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	2 clinvar	1 clinvar	4
missense			58 clinvar	3 clinvar		61
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	62	5	1	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024766.5	RefSeq	NP_079042.1	11	MANE Select
ENST00000378494.8	Ensembl	ENSP00000367755.3	11	MANE Select
ENST00000402247.5	Ensembl	ENSP00000385587.1	4	Standard
ENST00000402247.6	Ensembl	ENSP00000385587.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysine degradation - Homo sapiens (human)
Signaling by GPCR
Signal Transduction
Post-translational protein modification
Metabolism of proteins

Biological Process

protein methylation
mitochondrion organization
peptidyl-lysine methylation
regulation of rhodopsin mediated signaling pathway

Molecular Function

calmodulin-lysine N-methyltransferase activity
heat shock protein binding

Cellular Component

nucleus
cytoplasm
Golgi apparatus
cytosol
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378494
Coding exons: 11
Length: 410643
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125747
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.137	165	160	1.03	0.00000768	2090
Missense (PolyPhen)		30	35.97	0.83404		464
Synonymous	0.368	56	59.6	0.939	0.00000286	611
Loss of Function	-0.286	22	20.6	1.07	0.00000115	237

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00055	0.00054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00024	0.00023	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the trimethylation of 'Lys-116' in calmodulin. {ECO:0000269|PubMed:20975703}.;

Intolerance Scores

RVIS EVS: -0.45
RVIS percentile EVS: 24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): 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