NCALD

neurocalcin delta, the group of EF-hand domain containing

Basic information

Region (hg38): 8:101686541-102124907

Links

ENSG00000104490 ∙ NCBI:83988 ∙ OMIM:606722 ∙ HGNC:7655 ∙ Uniprot:P61601 ∙ 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 NCALD gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

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

Variants in NCALD

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

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

Position	Type	Phenotype	Significance	ClinVar
8-101689356-T-C		not specified	Uncertain significance (Jan 30, 2024)
8-101692819-G-C		not specified	Uncertain significance (Dec 18, 2023)
8-101692836-T-C		not specified	Uncertain significance (Dec 19, 2022)
8-101692860-G-C		not specified	Uncertain significance (Dec 20, 2023)
8-102124496-GC-G			Benign (Nov 01, 2022)
8-102124506-T-A			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCALD	protein_coding	protein_coding	ENST00000395923	3	438365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.893	0.106	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	70	118	0.595	0.00000675	1295
Missense in Polyphen		12	36.568	0.32815		451
Synonymous	-0.147	46	44.8	1.03	0.00000290	333
Loss of Function	2.50	0	7.25	0.00	3.03e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. Binds three calcium ions.
• Pathway: Olfactory transduction - Homo sapiens (human);Activation of Ca-permeable Kainate Receptor;Ionotropic activity of kainate receptors;Activation of kainate receptors upon glutamate binding;Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.0673
• hipred: Y
• hipred_score: 0.830
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncald
• Phenotype: vision/eye phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ncaldb
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: regulation of systemic arterial blood pressure;vesicle-mediated transport;calcium-mediated signaling
• Cellular component: cytosol;clathrin coat of trans-Golgi network vesicle
• Molecular function: actin binding;calcium ion binding;protein binding;tubulin binding;clathrin binding;alpha-tubulin binding