LCE1C

Chr 1

late cornified envelope 1C

ENSG00000197084 UniProt: Q5T751 OMIM: 612605

Precursors of the cornified envelope of the stratum corneum

OMIM Research

Precursors of the cornified envelope of the stratum corneum

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.86

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

ncbi: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.86LOEUF

pLI 0.028

Z-score 0.12

OE 0.91 (0.34–1.86)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.57Z-score

OE missense 1.20 (1.00–1.44)

80 obs / 66.8 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.91 (0.34–1.86)

0≤0.351.4

Missense OE?1.20 (1.00–1.44)

0≤0.61.4

Synonymous OE?1.95

0≤1.21.6

LoF obs/exp: 2 / 2.2Missense obs/exp: 80 / 66.8Syn Z: -3.89

Background carrier burden — how many people carry a rare variant somewhere in LCE1C?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 190

154 rare PASS variants

Rare truncating (LoF)

1 in 2,200

28 rare PASS variants

Rare synonymous (reference)

1 in 360

75 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for LCE1C. 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 370	1 in 5,100
South Asian	~43k	1 in 490	1 in 3,300
Remaining (unassigned)	~30k	1 in 170	1 in 3,800
European (Finnish)	~27k	1 in 3,800	1 in 940
Admixed American	~22k	1 in 250	1 in 2,100
African / African American	~21k	1 in 220	1 in 1,000
East Asian	~20k	1 in 170	≈ 1 in 6,600
Ashkenazi Jewish	~13k	≈ 1 in 4,400	none seen
Middle Eastern	~2,883	1 in 160	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): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓