ZDHHC19

zinc finger DHHC-type palmitoyltransferase 19, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 3:196197452-196211437

Links

ENSG00000163958 ∙ NCBI:131540 ∙ OMIM:618671 ∙ HGNC:20713 ∙ Uniprot:Q8WVZ1 ∙ 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 ZDHHC19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC19 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				1		1
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in ZDHHC19

This is a list of pathogenic ClinVar variants found in the ZDHHC19 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196198303-C-A		not specified	Uncertain significance (Nov 22, 2021)
3-196198369-G-A		not specified	Uncertain significance (Jun 16, 2024)
3-196198372-A-G		not specified	Uncertain significance (Jul 12, 2023)
3-196198838-C-G		not specified	Uncertain significance (Nov 15, 2021)
3-196198841-G-T		not specified	Uncertain significance (Feb 26, 2024)
3-196198844-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-196198870-C-T		not specified	Uncertain significance (Oct 21, 2024)
3-196207421-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-196207475-G-C		not specified	Uncertain significance (Jan 16, 2025)
3-196208466-G-A		not specified	Uncertain significance (Oct 06, 2021)
3-196208497-T-G		not specified	Uncertain significance (Jan 24, 2025)
3-196208506-G-C		not specified	Uncertain significance (Oct 05, 2022)
3-196208529-T-A		not specified	Uncertain significance (Dec 20, 2023)
3-196209420-G-A		not specified	Uncertain significance (Feb 26, 2025)
3-196209422-C-T		not specified	Uncertain significance (Dec 24, 2024)
3-196209423-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-196209448-T-G		not specified	Uncertain significance (Feb 06, 2023)
3-196209455-C-T		not specified	Uncertain significance (Apr 19, 2024)
3-196209456-G-A		not specified	Uncertain significance (Nov 20, 2023)
3-196209485-T-C		not specified	Uncertain significance (Oct 05, 2023)
3-196209491-G-A		not specified	Likely benign (Feb 19, 2025)
3-196210655-C-T		not specified	Likely benign (Jan 23, 2023)
3-196210667-A-G		not specified	Uncertain significance (Jan 08, 2025)
3-196210669-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-196210681-A-G		not specified	Uncertain significance (Dec 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC19	protein_coding	protein_coding	ENST00000296326	7	13989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00718	0.978	124823	0	36	124859	0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	138	182	0.757	0.0000104	1980
Missense in Polyphen		41	54.497	0.75234		644
Synonymous	-0.0518	79	78.4	1.01	0.00000483	645
Loss of Function	2.13	6	14.9	0.404	8.06e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000245
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000115
Middle Eastern	0.000278	0.000278
South Asian	0.000362	0.000360
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0878

Intolerance Scores

• loftool: 0.628
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

• pHI: 0.0650
• hipred: N
• hipred_score: 0.172
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.612

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc19

Gene ontology

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