ZDHHC12

zinc finger DHHC-type palmitoyltransferase 12, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 9:128720869-128724127

Links

ENSG00000160446 ∙ NCBI:84885 ∙ ∙ HGNC:19159 ∙ Uniprot:Q96GR4 ∙ 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 ZDHHC12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC12 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			22			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	22	0	0

Variants in ZDHHC12

This is a list of pathogenic ClinVar variants found in the ZDHHC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128721258-A-G		not specified	Uncertain significance (Aug 22, 2023)
9-128721261-A-C		not specified	Uncertain significance (May 18, 2023)
9-128721275-C-A		not specified	Uncertain significance (Mar 27, 2023)
9-128721329-C-A		not specified	Uncertain significance (Jul 12, 2022)
9-128721341-A-G		not specified	Uncertain significance (Dec 03, 2021)
9-128721359-G-T		not specified	Uncertain significance (May 24, 2024)
9-128721386-G-C		not specified	Uncertain significance (Feb 27, 2024)
9-128721768-C-T		not specified	Uncertain significance (Jul 14, 2023)
9-128721771-C-T		not specified	Uncertain significance (May 27, 2022)
9-128721776-G-C		not specified	Uncertain significance (Mar 29, 2022)
9-128721783-C-T		not specified	Uncertain significance (Oct 12, 2021)
9-128721784-G-A		not specified	Uncertain significance (Feb 28, 2023)
9-128721817-G-C		not specified	Uncertain significance (Dec 08, 2023)
9-128722032-G-A		not specified	Uncertain significance (Oct 22, 2021)
9-128722034-C-T		not specified	Uncertain significance (Jun 11, 2021)
9-128722049-G-A		not specified	Uncertain significance (Sep 26, 2022)
9-128722050-G-A		not specified	Uncertain significance (Nov 15, 2021)
9-128722442-G-A		not specified	Uncertain significance (Mar 21, 2023)
9-128722488-C-T		not specified	Uncertain significance (May 30, 2024)
9-128722536-G-T		not specified	Uncertain significance (Jan 04, 2024)
9-128722556-T-C		not specified	Uncertain significance (Jun 30, 2022)
9-128722559-T-G		not specified	Uncertain significance (Jun 17, 2024)
9-128722568-C-T		not specified	Uncertain significance (Feb 16, 2023)
9-128724048-C-G		not specified	Uncertain significance (Mar 19, 2024)
9-128724065-C-G		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC12	protein_coding	protein_coding	ENST00000372663	5	3259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000529	0.897	125655	0	54	125709	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.340	143	155	0.923	0.00000948	1641
Missense in Polyphen		62	63.632	0.97435		706
Synonymous	0.518	62	67.4	0.920	0.00000372	581
Loss of Function	1.45	7	12.5	0.558	6.21e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000792	0.000754
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000246	0.000237
Middle Eastern	0.00	0.00
South Asian	0.0000685	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.557
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.1

Haploinsufficiency Scores

• pHI: 0.0733
• hipred: N
• hipred_score: 0.231
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.701

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc12

Gene ontology

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