CALY

calcyon neuron specific vesicular protein

Basic information

Region (hg38): 10:133324072-133336935

Previous symbols: [ "DRD1IP" ]

Links

ENSG00000130643 ∙ NCBI:50632 ∙ OMIM:604647 ∙ HGNC:17938 ∙ Uniprot:Q9NYX4 ∙ 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 CALY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALY 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in CALY

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

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

Position	Type	Phenotype	Significance	ClinVar
10-133325868-G-A		not specified	Uncertain significance (Jan 17, 2024)
10-133325897-G-T		not specified	Uncertain significance (Oct 03, 2023)
10-133325906-G-C		not specified	Uncertain significance (Jan 05, 2022)
10-133325976-A-T		not specified	Uncertain significance (Mar 17, 2023)
10-133326019-G-T		not specified	Uncertain significance (Jul 25, 2024)
10-133326052-G-T		not specified	Uncertain significance (Jun 18, 2021)
10-133326112-G-A			Likely benign (Jun 01, 2022)
10-133326933-A-G		not specified	Uncertain significance (Nov 29, 2021)
10-133326946-A-G		not specified	Uncertain significance (Sep 01, 2024)
10-133326982-C-A		not specified	Uncertain significance (Aug 11, 2024)
10-133327909-C-T		not specified	Uncertain significance (Nov 17, 2023)
10-133327919-C-T		not specified	Uncertain significance (Apr 25, 2023)
10-133328015-C-T		not specified	Uncertain significance (Mar 16, 2022)
10-133328923-C-G		not specified	Uncertain significance (Apr 04, 2024)
10-133328933-C-G		not specified	Uncertain significance (Dec 20, 2023)
10-133328970-C-A		not specified	Uncertain significance (Jun 10, 2022)
10-133328973-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-133328977-C-T		not specified	Uncertain significance (Oct 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALY	protein_coding	protein_coding	ENST00000252939	4	11549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0387	0.848	124728	0	3	124731	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	67	103	0.650	0.00000548	1375
Missense in Polyphen		20	41.572	0.4811		489
Synonymous	0.318	41	43.7	0.939	0.00000239	439
Loss of Function	1.28	3	6.52	0.460	2.78e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000105	0.000100
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000178
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with clathrin light chain A and stimulates clathrin self-assembly and clathrin-mediated endocytosis. {ECO:0000269|PubMed:16595675}.
• Pathway: Dopaminergic synapse - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.131

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.379
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.245

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Caly
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: dopamine receptor signaling pathway;endosomal transport;positive regulation of endocytosis;clathrin coat assembly;postsynaptic neurotransmitter receptor internalization
• Cellular component: endosome;integral component of plasma membrane;cytoplasmic vesicle membrane;cytoplasmic vesicle;postsynaptic endocytic zone;glutamatergic synapse
• Molecular function: protein binding;clathrin light chain binding;cargo receptor activity;protein-containing complex binding