NUP62CL

Chr X

nucleoporin 62 C-terminal like

NCBI Gene: 54830 ENSG00000198088 UniProt: Q9H1M0

This gene encodes a protein containing a nucleoporin domain, which are glycoproteins that form nuclear pore complexes responsible for transport between the nucleus and cytoplasm. The gene is not highly constrained against loss-of-function variants (pLI = 0.001, LOEUF = 1.49), and no well-established disease associations have been reported in the provided data.

ResearchSummary from RefSeq

This gene encodes a protein containing a domain found in nucleoporins which are glycoproteins found in nuclear pore complexes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.49

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.49LOEUF

pLI 0.001

Z-score 0.68

OE 0.72 (0.38–1.49)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.27Z-score

OE missense 0.90 (0.72–1.13)

54 obs / 59.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.72 (0.38–1.49)

0≤0.351.4

Missense OE?0.90 (0.72–1.13)

0≤0.61.4

Synonymous OE?0.80

0≤1.21.6

LoF obs/exp: 5 / 6.9Missense obs/exp: 54 / 59.8Syn Z: 0.78

Background carrier burden — how many people carry a rare variant somewhere in NUP62CL?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 220

201 rare PASS variants

Rare truncating (LoF)

1 in 970

37 rare PASS variants

Rare synonymous (reference)

1 in 1,200

73 rare PASS variants

Rare missense and truncating variants are carried at similar rates in NUP62CL; this gene does not show strong loss-of-function constraint by this measure. 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)	~560k	1 in 460	1 in 880
South Asian	~36k	1 in 190	1 in 1,900
Remaining (unassigned)	~31k	1 in 340	1 in 1,000
European (Finnish)	~27k	1 in 1,700	≈ 1 in 9,000
Admixed American	~23k	1 in 270	1 in 910
African / African American	~21k	1 in 280	1 in 2,000
East Asian	~20k	1 in 210	≈ 1 in 20,000
Ashkenazi Jewish	~13k	≈ 1 in 6,400	≈ 1 in 11,000
Middle Eastern	~2,755	1 in 210	≈ 1 in 920

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): 5 of 6 coding exons well covered in gnomAD exomes; exon 6 marginal. Genomes: all 6.? see exons ↓