ZACN

zinc activated ion channel, the group of Zinc activated channels

Basic information

Region (hg38): 17:76071961-76083666

Previous symbols: [ "LGICZ1" ]

Links

ENSG00000186919

∙ NCBI:353174 ∙ OMIM:610935 ∙ HGNC:29504 ∙ Uniprot:Q401N2 ∙ 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 ZACN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZACN gene is commonly pathogenic or not. These statistics are base on trasncript: . Only rare variants are included in the table.

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			36 clinvar	7 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	7	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZACN	protein_coding	protein_coding	ENST00000334586	9	11706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-22	0.0000246	80560	6597	38590	125747	0.200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	257	239	1.08	0.0000136	2635
Missense in Polyphen		71	61.877	1.1474		749
Synonymous	-0.996	122	109	1.12	0.00000666	873
Loss of Function	-2.13	27	17.4	1.55	8.63e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.488	0.486
Ashkenazi Jewish	0.156	0.156
East Asian	0.365	0.365
Finnish	0.178	0.177
European (Non-Finnish)	0.173	0.172
Middle Eastern	0.365	0.365
South Asian	0.123	0.122
Other	0.201	0.201

dbNSFP

Source: dbNSFP

Function: FUNCTION: Zinc-activated ligand-gated ion channel. {ECO:0000269|PubMed:12381728}.;

Intolerance Scores

loftool: 0.505
rvis_EVS: 0.62
rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

pHI: 0.0533
hipred: N
hipred_score: 0.180
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0524

Gene Damage Prediction

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

Gene ontology

Biological process: signal transduction;chemical synaptic transmission;response to zinc ion;ion transmembrane transport;regulation of membrane potential;nervous system process
Cellular component: plasma membrane;integral component of plasma membrane;neuron projection;synapse
Molecular function: transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;zinc ion binding;ligand-gated ion channel activity