ZDHHC13

zinc finger DHHC-type palmitoyltransferase 13, the group of Zinc fingers DHHC-type|Ankyrin repeat domain containing

Basic information

Region (hg38): 11:19117099-19176422

Links

ENSG00000177054 ∙ NCBI:54503 ∙ OMIM:612815 ∙ HGNC:18413 ∙ Uniprot:Q8IUH4 ∙ 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 ZDHHC13 gene.

• not_specified (82 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019028.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1		2
missense			84	3		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6			6
Total	0	0	91	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC13	protein_coding	protein_coding	ENST00000446113	17	59324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124530	0	108	124638	0.000433

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.752	256	292	0.876	0.0000133	4057
Missense in Polyphen		74	81.52	0.90776		1155
Synonymous	-0.228	103	100	1.03	0.00000449	1132
Loss of Function	0.512	31	34.2	0.906	0.00000175	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000944
Ashkenazi Jewish	0.000698	0.000696
East Asian	0.000418	0.000389
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000528	0.000513
Middle Eastern	0.000418	0.000389
South Asian	0.000437	0.000425
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase for HTT and GAD2. May play a role in Mg(2+) transport. {ECO:0000250|UniProtKB:Q9CWU2}.

Recessive Scores

• pRec: 0.0740

Intolerance Scores

• loftool: 0.938
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000672

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: zdhhc13
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: positive regulation of I-kappaB kinase/NF-kappaB signaling;magnesium ion transmembrane transport
• Cellular component: Golgi membrane;endoplasmic reticulum;membrane;integral component of membrane;cytoplasmic vesicle membrane;Golgi-associated vesicle membrane
• Molecular function: magnesium ion transmembrane transporter activity;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity