ZDHHC16

zinc finger DHHC-type palmitoyltransferase 16, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 10:97446170-97457370

Links

ENSG00000171307 ∙ NCBI:84287 ∙ OMIM:616750 ∙ HGNC:20714 ∙ Uniprot:Q969W1 ∙ 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 ZDHHC16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC16 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in ZDHHC16

This is a list of pathogenic ClinVar variants found in the ZDHHC16 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97451713-G-A		not specified	Uncertain significance (Apr 07, 2023)
10-97451724-C-G		not specified	Uncertain significance (Oct 13, 2021)
10-97451724-C-T		not specified	Uncertain significance (Jun 07, 2024)
10-97451775-G-A		not specified	Uncertain significance (Nov 14, 2023)
10-97451776-G-A		not specified	Uncertain significance (Mar 02, 2023)
10-97451853-G-A		not specified	Uncertain significance (Mar 19, 2024)
10-97451905-G-A		not specified	Uncertain significance (May 18, 2023)
10-97451909-G-C		not specified	Uncertain significance (Feb 16, 2023)
10-97452133-C-T		not specified	Uncertain significance (Jun 11, 2021)
10-97452136-T-C		not specified	Uncertain significance (Feb 06, 2024)
10-97452414-G-C			Uncertain significance (Mar 01, 2017)
10-97452430-G-A		not specified	Uncertain significance (Mar 02, 2023)
10-97452450-G-C		not specified	Uncertain significance (Mar 05, 2024)
10-97452925-T-C		Intellectual disability	Pathogenic (Feb 20, 2024)
10-97453814-G-A		not specified	Uncertain significance (Jan 06, 2023)
10-97454748-T-G		not specified	Uncertain significance (Aug 12, 2021)
10-97454751-G-A		not specified	Uncertain significance (Mar 17, 2023)
10-97455998-G-A		not specified	Uncertain significance (Jul 09, 2021)
10-97456833-T-C		not specified	Uncertain significance (Jun 24, 2022)
10-97456872-CCT-C		Intellectual disability;Neurodevelopmental abnormality	Pathogenic (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC16	protein_coding	protein_coding	ENST00000393760	10	11201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000165	0.999	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.774	200	233	0.857	0.0000142	2444
Missense in Polyphen		64	83.677	0.76484		937
Synonymous	-0.161	89	87.1	1.02	0.00000491	764
Loss of Function	2.82	11	26.8	0.411	0.00000173	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000337
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyl acyltransferase that mediates palmitoylation of proteins such as PLN and ZDHHC6 (PubMed:28826475). Required during embryonic heart development and cardiac function, possibly by mediating palmitoylation of PLN, thereby affecting PLN phosphorylation and homooligomerization (By similarity). Also required for eye development (By similarity). Palmitoylates ZDHHC6, affecting the quaternary assembly of ZDHHC6, its localization, stability and function (PubMed:28826475). May play a role in DNA damage response (By similarity). May be involved in apoptosis regulation (By similarity). Involved in the proliferation of neural stem cells by regulating the FGF/ERK pathway (By similarity). {ECO:0000250|UniProtKB:B8A4F0, ECO:0000250|UniProtKB:Q9ESG8, ECO:0000269|PubMed:28826475}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.470
• rvis_EVS: -0.91
• rvis_percentile_EVS: 9.9

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.343
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc16
• Phenotype: growth/size/body region phenotype; muscle phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: zdhhc16a
• Affected structure: anterior neural plate
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

• Biological process: eye development;apoptotic process;cellular response to DNA damage stimulus;heart development;protein palmitoylation;telencephalon development
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane
• Molecular function: protein binding;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity