ZDHHC20

Chr 13

zDHHC palmitoyltransferase 20

Also known as: 4933421L13Rik, DHHC-20, DHHC20

NCBI Gene: 253832 ENSG00000180776 UniProt: Q5W0Z9

ZDHHC20 encodes a palmitoyltransferase that catalyzes the addition of palmitate to cysteine residues in various protein substrates, including EGFR and CALHM1, thereby modulating protein localization and signaling. The gene shows low constraint to loss-of-function variants (pLI 0.0005, LOEUF 0.747), suggesting high tolerance to protein-truncating mutations. Disease associations and inheritance patterns for ZDHHC20 mutations have not been established in the provided data.

ResearchSummary from RefSeq, UniProt

Enables protein-cysteine S-palmitoyltransferase activity and zinc ion binding activity. Involved in DNA damage response and peptidyl-L-cysteine S-palmitoylation. Located in Golgi membrane; nucleus; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.75

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.75LOEUF

pLI 0.001

Z-score 2.43

OE 0.43 (0.26–0.75)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.25Z-score

OE missense 0.73 (0.63–0.85)

125 obs / 171.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.43 (0.26–0.75)

0≤0.351.4

Missense OE?0.73 (0.63–0.85)

0≤0.61.4

Synonymous OE?0.89

0≤1.21.6

LoF obs/exp: 9 / 21.0Missense obs/exp: 125 / 171.1Syn Z: 0.69

Background carrier burden — how many people carry a rare variant somewhere in ZDHHC20?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 220

414 rare PASS variants

Rare truncating (LoF)

1 in 1,600

109 rare PASS variants

Rare synonymous (reference)

1 in 480

176 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ZDHHC20. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 390	1 in 1,800
South Asian	~43k	1 in 200	1 in 1,000
Remaining (unassigned)	~30k	1 in 120	1 in 1,500
European (Finnish)	~27k	1 in 700	1 in 2,600
Admixed American	~22k	1 in 140	1 in 970
African / African American	~21k	1 in 120	1 in 3,000
East Asian	~20k	1 in 120	1 in 1,400
Ashkenazi Jewish	~13k	≈ 1 in 6,500	≈ 1 in 3,100
Middle Eastern	~2,884	1 in 180	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 8 of 12 coding exons well covered in gnomAD exomes; exon 2 poorly covered; exons 6, 9, 12 marginal. Genomes: all 12.? see exons ↓