CALN1

calneuron 1, the group of EF-hand domain containing

Basic information

Region (hg38): 7:71779490-72447151

Links

ENSG00000183166 ∙ NCBI:83698 ∙ OMIM:607176 ∙ HGNC:13248 ∙ Uniprot:Q9BXU9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CALN1 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALN1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	1

Variants in CALN1

This is a list of pathogenic ClinVar variants found in the CALN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-71787867-G-A		not specified	Uncertain significance (Dec 17, 2021)
7-71810328-G-T			Benign (Aug 15, 2017)
7-71810392-T-C		not specified	Uncertain significance (Jun 10, 2022)
7-71810446-T-G		not specified	Uncertain significance (Dec 19, 2022)
7-72023704-C-T		not specified	Uncertain significance (Jan 09, 2024)
7-72106158-G-C			Uncertain significance (Sep 01, 2022)
7-72106206-C-T			Benign (Aug 15, 2017)
7-72106237-T-G		not specified	Uncertain significance (Oct 13, 2023)
7-72278725-T-C		not specified	Uncertain significance (Apr 28, 2023)
7-72278779-C-T		not specified	Uncertain significance (Jan 17, 2023)
7-72278781-G-A		not specified	Uncertain significance (May 05, 2023)
7-72403284-G-A		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALN1	protein_coding	protein_coding	ENST00000395275	6	667661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0319	0.960	125737	0	7	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	109	166	0.655	0.0000103	1737
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.344
• hipred: N
• hipred_score: 0.459
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Caln1

Gene ontology

• Cellular component: plasma membrane;integral component of membrane;trans-Golgi network membrane;perinuclear region of cytoplasm
• Molecular function: calcium ion binding