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.

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	7		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	7	0

Variants in ZACN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-76072306-A-G		Neutropenia, severe congenital, 10, autosomal recessive	Pathogenic (Oct 04, 2023)
17-76072331-A-G		not specified	Uncertain significance (Jan 30, 2024)
17-76072332-A-T		not specified	Uncertain significance (Oct 20, 2023)
17-76072365-G-C		not specified	Uncertain significance (Sep 20, 2023)
17-76072413-T-C		not specified	Uncertain significance (Dec 14, 2022)
17-76072415-C-A		not specified	Uncertain significance (Jun 23, 2023)
17-76072418-C-A		not specified	Uncertain significance (May 05, 2023)
17-76074890-G-A		not specified	Uncertain significance (Dec 12, 2023)
17-76074893-T-C		not specified	Uncertain significance (Jul 15, 2021)
17-76074894-C-T		not specified	Uncertain significance (Dec 20, 2023)
17-76074991-C-G		not specified	Uncertain significance (Oct 08, 2024)
17-76075010-A-C		not specified	Uncertain significance (Sep 03, 2024)
17-76075032-T-G		not specified	Uncertain significance (Nov 06, 2023)
17-76075094-G-C		not specified	Uncertain significance (Jul 08, 2024)
17-76075097-C-A		not specified	Uncertain significance (Feb 27, 2023)
17-76075122-C-T		not specified	Uncertain significance (May 17, 2023)
17-76075211-C-A		not specified	Uncertain significance (Dec 02, 2021)
17-76075213-C-G		not specified	Uncertain significance (Nov 11, 2024)
17-76075234-C-A			Likely benign (Aug 15, 2018)
17-76076649-C-A		not specified	Uncertain significance (Jun 22, 2024)
17-76076685-C-G		not specified	Uncertain significance (Sep 13, 2023)
17-76076780-C-A		not specified	Uncertain significance (May 26, 2023)
17-76076815-G-A		not specified	Uncertain significance (Feb 17, 2022)
17-76076851-G-A		not specified	Uncertain significance (Apr 24, 2024)
17-76076857-T-C		not specified	Uncertain significance (Aug 01, 2024)

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

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