NUP107

Chr 12AR

nucleoporin 107

Also known as: GAMOS7, NPHS11, NUP84, ODG6, ODG6; GAMOS7

NCBI Gene: 57122 ENSG00000111581 UniProt: P57740 OMIM: 607617

The protein is an essential component of the nuclear pore complex that controls molecular transport between the nucleus and cytoplasm and is involved in kidney development. Mutations cause autosomal recessive conditions including Galloway-Mowat syndrome, nephrotic syndrome, and ovarian dysgenesis, primarily affecting the kidneys and reproductive system. The gene is highly intolerant to loss-of-function variants (LOEUF 0.57), indicating that complete loss of protein function is likely pathogenic.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a member of the nucleoporin family. The protein is localized to the nuclear rim and is an essential component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

?Ovarian dysgenesis 6MIM #618078

Galloway-Mowat syndrome 7MIM #618348

Nephrotic syndrome, type 11MIM #616730

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Galloway-Mowat syndrome 7; Nephrotic syndrome, type 11; no ClinGen or GenCC tier

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.57

LOEUF

LOF

Mechanism· G2P

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.57LOEUF

pLI 0.000

Z-score 4.34

OE 0.41 (0.30–0.57)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.89Z-score

OE missense 0.76 (0.70–0.83)

373 obs / 490.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.41 (0.30–0.57)

0≤0.351.4

Missense OE?0.76 (0.70–0.83)

0≤0.61.4

Synonymous OE?0.91

0≤1.21.6

LoF obs/exp: 26 / 63.3Missense obs/exp: 373 / 490.5Syn Z: 0.91

Background carrier burden — how many people carry a rare variant somewhere in NUP107?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 73

1,029 rare PASS variants

Rare truncating (LoF)

1 in 850

223 rare PASS variants

Rare synonymous (reference)

1 in 180

333 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NUP107. 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 85	1 in 880
South Asian	~43k	1 in 56	1 in 520
Remaining (unassigned)	~30k	1 in 71	1 in 1,100
European (Finnish)	~27k	1 in 140	1 in 2,200
Admixed American	~22k	1 in 55	1 in 1,200
African / African American	~21k	1 in 54	1 in 730
East Asian	~20k	1 in 76	1 in 450
Ashkenazi Jewish	~13k	1 in 540	1 in 500
Middle Eastern	~2,884	1 in 99	≈ 1 in 950

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): 16 of 28 coding exons well covered in gnomAD exomes; exons 6, 8, 9, 10, 12 and 7 more marginal. Genomes: all 28.? see exons ↓