PDXDC1

Chr 16

pyridoxal dependent decarboxylase domain containing 1

Also known as: LP8165

NCBI Gene: 23042 ENSG00000179889 UniProt: Q6P996

The PDXDC1 protein enables cadherin binding and is involved in carboxylic acid metabolism, with localization to the Golgi apparatus. Mutations in this gene have not been definitively associated with human disease based on the provided information. The gene shows relatively low constraint against loss-of-function variants.

ResearchSummary from RefSeq

Enables cadherin binding activity. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.85

LOEUF

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?

0.85LOEUF

pLI 0.000

Z-score 2.35

OE 0.61 (0.44–0.85)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.47Z-score

OE missense 0.94 (0.86–1.02)

397 obs / 424.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.61 (0.44–0.85)

0≤0.351.4

Missense OE?0.94 (0.86–1.02)

0≤0.61.4

Synonymous OE?1.06

0≤1.21.6

LoF obs/exp: 25 / 41.3Missense obs/exp: 397 / 424.0Syn Z: -0.56

Background carrier burden — how many people carry a rare variant somewhere in PDXDC1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 41

889 rare PASS variants

Rare truncating (LoF)

1 in 520

142 rare PASS variants

Rare synonymous (reference)

1 in 63

368 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PDXDC1. 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 69	1 in 520
South Asian	~43k	1 in 34	1 in 510
Remaining (unassigned)	~30k	1 in 41	1 in 290
European (Finnish)	~27k	1 in 170	1 in 1,300
Admixed American	~22k	1 in 38	1 in 390
African / African American	~21k	1 in 28	1 in 670
East Asian	~20k	1 in 40	1 in 690
Ashkenazi Jewish	~13k	1 in 150	≈ 1 in 6,400
Middle Eastern	~2,884	1 in 59	≈ 1 in 1,400

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): 20 of 23 coding exons well covered in gnomAD exomes; exons 1, 18, 22 marginal. Genomes: all 23.? see exons ↓