CALN1

protein-coding

calneuron 1, the group of EF-hand domain containing

Gene summary

This gene encodes a protein with high similarity to the calcium-binding proteins of the calmodulin family. The encoded protein contains two EF-hand domains and potential calcium-binding sites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

MANE transcript

NM_031468.4

Inheritance

—

ClinVar variants

U:28B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr7:71,779,491-72,447,151

External References & Databases

Ensembl (ENSG00000183166)

Transcript & Mutation Effects

hg38 • Region Span ~667.7 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 CALN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031468.4. 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			1 clinvar		1 clinvar	2
missense			26 clinvar			26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	28	0	1	29

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031468.4	RefSeq	NP_113656.2	6	MANE Select
ENST00000395275.7	Ensembl	ENSP00000378690.2	6	MANE Select
NM_001017440.3	RefSeq	NP_001017440.1	5	Standard
NM_001363460.1	RefSeq	NP_001350389.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding

Cellular Component

plasma membrane
integral component of membrane
trans-Golgi network membrane
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395275
Coding exons: 6
Length: 667661
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125744
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.58	109	166	0.655	0.0000103	1737
Missense (PolyPhen)		30	58.921	0.50916		600
Synonymous	-1.52	83	67.1	1.24	0.00000476	476
Loss of Function	2.31	5	14.5	0.345	8.76e-7	139

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity (By similarity). May play a role in the physiology of neurons and is potentially important in memory and learning. {ECO:0000250}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.352
RVIS EVS: -0.03
RVIS percentile EVS: 51.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.450

Gene Damage Prediction

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