PODXL2

Chr 3

podocalyxin like 2

Also known as: EG, PODLX2

NCBI Gene: 50512 ENSG00000114631 UniProt: Q9NZ53 OMIM: 616627

This gene is a member of the CD34 family of cell surface transmembrane proteins, which are characterized by an N-terminal extracellular mucin domain, globular and stalk domains, a single pass transmembrane region, and a charged cytoplasmic tail. The encoded protein is a ligand for vascular selectins. [provided by RefSeq, Oct 2012]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.14

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.14LOEUF

pLI 0.999

Z-score 4.27

OE 0.00 (0.00–0.14)

Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?

0.91Z-score

OE missense 0.86 (0.78–0.95)

271 obs / 316.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.14)

0≤0.351.4

Missense OE?0.86 (0.78–0.95)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 0 / 21.2Missense obs/exp: 271 / 316.4Syn Z: 0.24

Background carrier burden — how many people carry a rare variant somewhere in PODXL2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 100

723 rare PASS variants

Rare truncating (LoF)

1 in 5,300

52 rare PASS variants

Rare synonymous (reference)

1 in 140

330 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PODXL2. 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 130	1 in 6,600
South Asian	~43k	1 in 63	1 in 8,100
Remaining (unassigned)	~30k	1 in 84	1 in 6,000
European (Finnish)	~27k	1 in 140	1 in 1,200
Admixed American	~22k	1 in 84	≈ 1 in 7,600
African / African American	~21k	1 in 69	≈ 1 in 4,300
East Asian	~20k	1 in 97	1 in 1,800
Ashkenazi Jewish	~13k	1 in 240	1 in 1,500
Middle Eastern	~2,884	1 in 69	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): 6 of 8 coding exons well covered in gnomAD exomes; exons 1, 5 marginal. Genomes: 7 of 8 (exon 1 below).? see exons ↓