ZDHHC23

zinc finger DHHC-type palmitoyltransferase 23, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 3:113947901-113965401

Links

ENSG00000184307 ∙ NCBI:254887 ∙ OMIM:617334 ∙ HGNC:28654 ∙ Uniprot:Q8IYP9 ∙ 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 ZDHHC23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC23 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in ZDHHC23

This is a list of pathogenic ClinVar variants found in the ZDHHC23 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-113948809-C-G		not specified	Uncertain significance (May 17, 2023)
3-113953851-G-A		not specified	Uncertain significance (Nov 03, 2023)
3-113953890-A-T		not specified	Uncertain significance (Aug 02, 2021)
3-113953941-A-C		not specified	Uncertain significance (Feb 22, 2023)
3-113953990-A-G		not specified	Uncertain significance (Apr 13, 2023)
3-113954006-C-A		not specified	Uncertain significance (Jun 07, 2023)
3-113954043-G-A		not specified	Uncertain significance (Mar 20, 2024)
3-113954062-C-G		not specified	Uncertain significance (Feb 01, 2023)
3-113954139-G-A		not specified	Likely benign (Dec 14, 2023)
3-113954154-A-T		not specified	Uncertain significance (Oct 25, 2023)
3-113954158-G-A		not specified	Uncertain significance (Mar 23, 2023)
3-113954212-C-T		not specified	Uncertain significance (Oct 27, 2023)
3-113954296-C-T		not specified	Uncertain significance (Mar 14, 2023)
3-113954349-C-T		not specified	Uncertain significance (Sep 26, 2023)
3-113954364-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-113954367-A-G		not specified	Uncertain significance (May 24, 2023)
3-113954369-A-G		not specified	Uncertain significance (Feb 28, 2023)
3-113954407-T-A		not specified	Uncertain significance (Jun 06, 2023)
3-113956463-T-G		not specified	Uncertain significance (Dec 16, 2023)
3-113958365-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-113958470-G-A		not specified	Uncertain significance (Dec 14, 2023)
3-113958487-C-G		not specified	Uncertain significance (Oct 16, 2023)
3-113960729-G-A		not specified	Uncertain significance (Aug 09, 2021)
3-113965214-C-T		not specified	Uncertain significance (Jan 27, 2022)
3-113965232-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC23	protein_coding	protein_coding	ENST00000330212	5	17501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.84e-12	0.0484	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.912	193	232	0.832	0.0000128	2656
Missense in Polyphen		70	87.516	0.79986		939
Synonymous	1.19	77	91.5	0.842	0.00000520	829
Loss of Function	0.157	18	18.7	0.961	0.00000110	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000582	0.0000582
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase that mediates palmitoylation of KCNMA1, regulating localization of KCNMA1 to the plasma membrane. May be involved in NOS1 regulation and targeting to the synaptic membrane. {ECO:0000269|PubMed:22399288}.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.684
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.472
• hipred: N
• hipred_score: 0.219
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc23
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: protein targeting to membrane;peptidyl-L-cysteine S-palmitoylation;protein palmitoylation;protein localization to plasma membrane
• Cellular component: cellular_component;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: molecular_function;protein-cysteine S-palmitoyltransferase activity