NUSAP1

Chr 15

nucleolar and spindle associated protein 1

Also known as: ANKT, BM037, LNP, NUSAP, PRO0310p1, Q0310, SAPL

NCBI Gene: 51203 ENSG00000137804 UniProt: Q9BXS6

NUSAP1 is a nucleolar-spindle-associated protein that plays a role in spindle microtubule organization (Raemaekers et al., 2003 [PubMed 12963707]).[supplied by OMIM, Jun 2009]

Research

NUSAP1 is a nucleolar-spindle-associated protein that plays a role in spindle microtubule organization (Raemaekers et al., 2003 [PubMed 12963707]).[supplied by OMIM, Jun 2009]

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

0.60

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

Moderate LoF intolerance

LoF Constraint?

0.60LOEUF

pLI 0.046

Z-score 2.89

OE 0.30 (0.16–0.60)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

0.63Z-score

OE missense 0.88 (0.78–0.99)

190 obs / 216.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.30 (0.16–0.60)

0≤0.351.4

Missense OE?0.88 (0.78–0.99)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 6 / 19.9Missense obs/exp: 190 / 216.0Syn Z: -0.08

Background carrier burden — how many people carry a rare variant somewhere in NUSAP1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

539 rare PASS variants

Rare truncating (LoF)

1 in 1,400

120 rare PASS variants

Rare synonymous (reference)

1 in 420

204 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NUSAP1. 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 1,600
South Asian	~43k	1 in 100	1 in 620
Remaining (unassigned)	~30k	1 in 60	1 in 720
European (Finnish)	~27k	1 in 740	≈ 1 in 13,000
Admixed American	~22k	1 in 73	1 in 860
African / African American	~21k	1 in 110	1 in 580
East Asian	~20k	1 in 92	1 in 3,200
Ashkenazi Jewish	~13k	1 in 2,100	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 160	≈ 1 in 700

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): 7 of 11 coding exons well covered in gnomAD exomes; exons 2, 5, 6, 10 marginal. Genomes: all 11.? see exons ↓