CALML6

protein-coding

calmodulin like 6, the group of EF-hand domain containing

Gene summary

Predicted to enable calcium ion binding activity and enzyme regulator activity. Predicted to be involved in microtubule cytoskeleton organization. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_138705.4

Inheritance

—

ClinVar variants

U:24B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr1:1,915,108-1,917,296

External References & Databases

Ensembl (ENSG00000169885)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 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 CALML6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138705.4. 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					2 clinvar	2
missense			23 clinvar		1 clinvar	24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	24	0	3	27

Loading ClinVar variants...

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_138705.4	RefSeq	NP_619650.2	6	MANE Select
ENST00000307786.8	Ensembl	ENSP00000304643.3	6	MANE Select
NM_001330313.2	RefSeq	NP_001317242.1	5	Standard
ENST00000378604.3	Ensembl	ENSP00000367867.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
Aldosterone synthesis and secretion - Homo sapiens (human)
Oxytocin signaling pathway - Homo sapiens (human)
Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
Pertussis - Homo sapiens (human)

Biological Process

calcium-mediated signaling
regulation of catalytic activity

Molecular Function

calcium ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000307786
Coding exons: 6
Length: 2470
Individuals with no LoFs: 125631
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125656
p: 0.0000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0515	102	103	0.986	0.00000573	1204
Missense (PolyPhen)		30	28.239	1.0624		352
Synonymous	-0.0276	43	42.8	1.01	0.00000312	302
Loss of Function	-0.332	11	9.88	1.11	4.19e-7	118

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.150

Intolerance Scores

LoFtool: 0.538
RVIS EVS: 0.13
RVIS percentile EVS: 63.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.333

Gene Damage Prediction

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