1. Panels
  2. Intellectual disability
  3. NUSAP1
Genes in panel
Prev Next
Regions in panel
Prev Next

Intellectual disability

Gene: NUSAP1

Amber List (moderate evidence)
NUSAP1 (nucleolar and spindle associated protein 1)
EnsemblGeneIds (GRCh38): ENSG00000137804
EnsemblGeneIds (GRCh37): ENSG00000137804
OMIM: 612818, Gene2Phenotype
NUSAP1 is in 4 panels

1 review

Luke Stuart (Genomics England Curator)

Green List (high evidence)

Comment on list classification: 4 patients with de novo truncating NMD-escaping variants and consistent phenotype reported. Sufficient evidence to promote to Green at the next GMS panel update.
Created: 29 Oct 2026, 2:32 p.m. | Last Modified: 29 Oct 2026, 2:32 p.m.
Panel Version: 11.70
Nonsense-mediated decay (NMD)-escaping truncating variants in NUSAP1 are associated with a syndromic neurodevelopmental phenotype characterised by congenital microcephaly, profound developmental impairment, neonatal-onset refractory epilepsy, and structural brain malformations.

Mo et al., 2023 (PMID 37005340). A de novo NUSAP1 variant, c.1209C>A, p.(Tyr403Ter), was identified by trio exome sequencing in two unrelated probands. Both had severe congenital microcephaly (<1st centile and <5th centile), severe/profound developmental delay, neonatal-onset refractory epilepsy, complex structural brain malformations, and hypotonia. Transcript studies suggested NMD-escape. Both cases were characterised by fetal anomalies on prenatal USS (microcephaly, agenesis of the CC, small hindbrain in individual II‐2 and microcephaly, inter‐hemispheric cyst in individual II‐1).

Jacob et al., 2026 (PMID 42706591): Trio exome and genome sequencing in two probands, ID#1 and ID#2, identified de novo heterozygous truncating variants in NUSAP1: c.1264C>T, p.(Arg422Ter), and c.1213C>T p.(Gln405Ter), respectively. Seizures began on the first day of life in ID#1 and on day 8 of life in ID#2; congenital microcephaly was also noted (<1st percentile in ID#1). Additional shared features included developmental delay, profound intellectual disability, and variable structural abnormalities on brain MRI. Both cases where characterised by abnormal fetal USS (intrauterine growth restriction and oligohydramnios in ID#1, and microcephaly and ventriculomegaly in ID#2).
The authors also reported unchanged NUSAP1 expression by RNA sequencing in one affected individual. They delineated a critical region at the 3′ end of NUSAP1, where nonsense variants introduce a premature termination codon and escape NMD. Such variants are absent from healthy controls (gnomAD), whereas frameshift variants producing C-terminal elongations appear tolerated, consistent with gene-level nonsense constraint (https://www.deciphergenomics.org/gene/NUSAP1/overview/protein-genomic-info)

Four unrelated affected individuals are reported (with three distinct de novo NMD-escaping truncating variants) and a consistent phenotype including severe-profound developmental impairment and intellectual disability, epilepsy, severe microcephaly, and structural brain anomalies. A green rating is recommended for intellectual disability, early onset or syndromic epilepsy, severe microcephaly, and fetal anomalies panels at the next GMS panel update.

NUSAP1 is not currently associated with any disease/ phenotype in OMIM, Gene2Phenotype, ClinGen (10/2026).
Sources: Literature
Created: 29 Oct 2026, 2:08 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
microcephaly(MONDO:0001149); neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities(MONDO:0030063)

Publications

Mode of pathogenicity
Other

Created: 29 Oct 2026, 2:08 p.m.

Panel version: 11.68

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • microcephaly(MONDO:0001149)
  • neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities(MONDO:0030063)
Tags
Q4_26_promote_green
OMIM
612818
Clinvar variants
Variants in NUSAP1
Penetrance
None
Publications
Mode of Pathogenicity
Other
Panels with this gene

History Filter Activity

29 Oct 2026, Gel status: 2

Entity classified by Genomics England curator

Luke Stuart (Genomics England Curator)

Gene: nusap1 has been classified as Amber List (Moderate Evidence).

29 Oct 2026, Gel status: 2

Entity classified by Genomics England curator

Luke Stuart (Genomics England Curator)

Gene: nusap1 has been classified as Amber List (Moderate Evidence).

29 Oct 2026, Gel status: 1

Created, Added New Source, Added Tag, Set mode of inheritance, Set publications, Set Phenotypes, Set mode of pathogenicity

Luke Stuart (Genomics England Curator)

gene: NUSAP1 was added gene: NUSAP1 was added to Intellectual disability. Sources: Literature Q4_26_promote_green tags were added to gene: NUSAP1. Mode of inheritance for gene: NUSAP1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: NUSAP1 were set to 37005340; 42706591 Phenotypes for gene: NUSAP1 were set to microcephaly(MONDO:0001149); neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities(MONDO:0030063) Mode of pathogenicity for gene: NUSAP1 was set to Other Review for gene: NUSAP1 was set to AMBER