ZDHHC24

zinc finger DHHC-type containing 24, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 11:66520636-66546235

Links

ENSG00000174165 ∙ NCBI:254359 ∙ ∙ HGNC:27387 ∙ Uniprot:Q6UX98 ∙ 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 ZDHHC24 gene.

• Bardet-Biedl syndrome (439 variants)
• Bardet-Biedl syndrome 1 (194 variants)
• not provided (59 variants)
• not specified (29 variants)
• Inborn genetic diseases (29 variants)
• BBS1-related condition (24 variants)
• Retinitis pigmentosa (9 variants)
• Retinal dystrophy (9 variants)
• Usher syndrome (1 variants)
• - (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC24 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	36	60	192	196	15	499
Total	36	60	199	197	15

Highest pathogenic variant AF is 0.0000131

Variants in ZDHHC24

This is a list of pathogenic ClinVar variants found in the ZDHHC24 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66520965-C-T			Benign (Jun 18, 2021)
11-66521250-T-G		Bardet-Biedl syndrome	Likely benign (Jun 16, 2023)
11-66521252-T-A		Bardet-Biedl syndrome	Likely benign (Aug 09, 2023)
11-66521252-T-C		Bardet-Biedl syndrome	Likely benign (Jul 10, 2023)
11-66521252-T-TG		Bardet-Biedl syndrome	Likely benign (Aug 29, 2023)
11-66521253-G-T		Bardet-Biedl syndrome	Likely benign (Jul 17, 2023)
11-66521254-C-T		not specified • Bardet-Biedl syndrome	Likely benign (Jan 24, 2024)
11-66521255-G-A		Bardet-Biedl syndrome	Likely benign (Oct 22, 2023)
11-66521255-G-T		Bardet-Biedl syndrome	Likely benign (Dec 02, 2023)
11-66521257-T-G		Bardet-Biedl syndrome	Likely benign (Jul 17, 2023)
11-66521259-CTTG-C		Bardet-Biedl syndrome	Likely benign (Oct 30, 2023)
11-66521261-T-C		Bardet-Biedl syndrome	Likely benign (Oct 30, 2015)
11-66521261-TGTTTGCAGATG-T		Retinal dystrophy • Bardet-Biedl syndrome • BBS1-related disorder	Pathogenic/Likely pathogenic (Feb 09, 2023)
11-66521262-G-C		not specified • Bardet-Biedl syndrome • Bardet-Biedl syndrome 1	Benign (Feb 01, 2024)
11-66521265-T-A		Bardet-Biedl syndrome	Uncertain significance (Sep 01, 2022)
11-66521266-G-A		Bardet-Biedl syndrome	Likely benign (May 28, 2023)
11-66521269-G-C		Bardet-Biedl syndrome • Bardet-Biedl syndrome 1	Pathogenic/Likely pathogenic (Jan 07, 2022)
11-66521271-T-C		Bardet-Biedl syndrome • Bardet-Biedl syndrome 1 • BBS1-related disorder	Uncertain significance (Jan 02, 2024)
11-66521272-G-A		Bardet-Biedl syndrome • Bardet-Biedl syndrome 1	Uncertain significance (Sep 27, 2022)
11-66521275-C-A		Bardet-Biedl syndrome	Uncertain significance (Nov 22, 2022)
11-66521275-C-T		Bardet-Biedl syndrome	Likely benign (Mar 29, 2023)
11-66521277-T-C		Bardet-Biedl syndrome	Uncertain significance (Mar 10, 2022)
11-66521278-TCC-T		Bardet-Biedl syndrome 1	Likely pathogenic (Dec 17, 2021)
11-66521280-C-T		Bardet-Biedl syndrome • Bardet-Biedl syndrome 1 • BBS1-related disorder	Uncertain significance (Nov 27, 2023)
11-66521284-C-T		Bardet-Biedl syndrome • BBS1-related disorder	Likely benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC24	protein_coding	protein_coding	ENST00000310442	3	25602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000421	0.662	125587	0	17	125604	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.288	149	159	0.936	0.00000948	1717
Missense in Polyphen		69	74.224	0.92962		811
Synonymous	0.768	69	77.6	0.889	0.00000461	669
Loss of Function	0.747	6	8.33	0.721	4.09e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000193	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000966	0.0000924
European (Non-Finnish)	0.0000845	0.0000793
Middle Eastern	0.00	0.00
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.339
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc24
• Phenotype: normal phenotype

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 binding;protein-cysteine S-palmitoyltransferase activity