Inheritance

Autosomal dominant

Prevalence

 <1 / 1 000 000

Source: ORPHA:597623

Rapid or full curation?

ClinGen / GenCC / BabySeq / HGMD / OMIM

ClinGen - none. GenCC - Strong (Invitae) and Moderate (Ambry) for AD neurodevelopmental disorder with regression, abnormal movements, loss of speech, and seizures. Same disease described in OMIM. BabySeq - None. HGMD - curated variants in clinical validity scoring below.

Clinical Validity Scoring Notes and points

Note this is a single exon gene, therefore the typical NMD predictive rule (stop upstream of last 50nt of penultimate exon) cannot be used. The native stop codon occurs at p.797

GnomAD pLOF LOEUF score is 0.55, indicating gene is constrained for pLOF variants.

Marcogliese 2018 PMID: 30057031. Scored the truncating variants.

• c.562C>T p.R188* - 0 alleles gAD v4. Truncating, non-NMD.

  • Patient 2 - Not confirmed de novo. Initial development normal, followed by regression. Clinical features include lack of speech since 11 years, wheelchair use sinc 9y, dysphagia at 10y and requires g-tube, staring spells, dystonia with no ataxia, mild changes on EEG observed twice but had two normal EEGs at age 9 and 14, Abnormal brain MRI. 1 POINT

  • Patient 3 - Same variant as above, de novo. Initial development normal, followed by regression. Motor regression, speech regression, non-ambulatory since age 10. Progressive dysphagia. Myoclonus at age 10y, ataxic gait at 6 y. Spasticity, cerebellar signs. Brain MRI initially normal, progressed to cerebral atrophy at 20y. 1.5 POINTS

• 379C>T Gln127* - absent gnomAD v4, Truncating, non-NMD. Patient 4, parents not tested, Developmental delays present, unsteady gait, silent aspiration with feeding tube, seizures at 6y, lower extremeity dystonia, abnormal EEG, normal brain MRI. 1 POINT

• c.376C>T(p.Gln126*) - absent gnomAD v4, truncating, non-NMD, de novo. Patient 5 - No developmental delays, motor regression onset between 5-10 years, requires wheelchair, seizures starting at age 10, ataxia, chroeoathetosis, dystoonia, nhyperreflexia, abnormal EEG, abnormal brain MRI. 1.5 POINTS

• Drosophila ortholog, developed a mutant fly. Gene in fly is on X chromosomes, mutant is hemizygous lethal in males. Gene is localized in the fly CNS. Knockdown resulted in semi-lethality. Partial knockdown showed progressive abnormalities in climbing and were bang sensitive at 30 days compared to controls. Fly eyes showed abnormalities. Scoring this evidence at 0.25 points for non-human organism, downgrading since the ortholog is not highly similar to humans and the phenotype is not a close replication of the phenotype in humans.

Tran Mau-Them 2019 PMID 30166628

• Similar phenotype described in Marcogliese - normal initial development followed by severe regression and epilepsy with variable CNS abnormalites. Table 1 shows the features. per text all variants de novo, so added 0.5 for each case.

• c.519C>G p.Tyr173* - absent gnomad v4, truncating non-NMD. In patients 1 and 5. 1.5x2= 3 POINTS

• 361C>T Gln121* - absent gnomad v4, truncating non-NMD. In patient 2. 1.5 POINTS

• 519C>G Tyr173* - absent gnomad v4, truncating non-NMD. In patient 5 - 1.5 points

• 962delC Ala321Glufs*24 - absent gnomad v4, truncating non-NMD. In patient 7 - 1.5 points

• Truncating variants at the 3' end of the protein -

  • 2122delG Ala708Profs*59 absent gnomad v4, truncating non-NMD. Patient 8 - 1.5 points

  • 2135_2136delGT p.Leu713Serfs*56 absent gnomad v4, truncating non-NMD. Patient 9 - 1.5 points

  • Not scoring Cys714Alafs*49 in patient 10, there is a lot of missing datapoints including c.

  • 2152delT, Cys718Alafs*48 absent gnomad v4, truncating non-NMD. Patient 11 - 1.5 points

• RNA analysis on patient derived fibroblasts confirmed that the truncations escaped NMD with a ratio of at least 1:1 with the WT allele, suggesting that the shorter proten might be translated (fig 1C)

•  

Functional:

PMID: 36476864 - Invitro human model, patient fibroblast cell lines. Western blot showed only a small or no reduction of IRF2BPL protein levels compared w/ healthy controls (used an antibody that only detects full length protein and not the truncated version). Generated induced neurons using patient cells and found that the protein mainly localized in the nucleus with faint cytoplasmic signal. Controls had exclusive nuclear localization. Then generated induced neuronal progenitory cells that were then differentiated into astrocytes. All patients exhibited an activiated phenotype with altered morphology and higher GFAP expression compared with controls. Cellular localization showed full length protein was mislocalized to cytoplasm in the form of smears or aggregates. Truncated protein was found to dimerize and mis-localize full length IRF2BPL - transfected HEK293 cells, a pull-down assay showed the IRF2BPL protein can dimerize with itself and that truncated isoforms are stable. Full length protein was redistributed to the cytoplasm in the form of aggregates when expressed with truncated protein forms. EXPERIMENTAL - 1 POINT PROTEIN INTERACTION, 1 POINT EXPRESSION

Replication over time:

Horovits 2023 PMID: 37346291 - several patients reported, scoring c.1099 G>T; p.Glu367Ter in patient 2, de novo, absent gnomAD, truncating, non-NMD.

Clinical Validity Points Total

>12 POINTS

Source: 30057031, 30166628, 37346291, 36476864

Clinical Validity Classification

Definitive

Source: 30057031, 30166628, 37346291, 36476864

Molecular Mechanism

Unknown - could be LOF, could be dominant negative. However, truncating variants are the primary variant type and have been reported across the entire gene. Therefore, propose using PM4_Strong provided that the stop codon is located within p.119 to 769

• c.355C>T p.Q119* in a case report with dystonia, saccades and seizures PMID: 31621620.

• 2135_2136delGT p.Leu713Serfs*56 absent gnomad v4, truncating non-NMD. Patient 9 - 1.5 points (PMID: Tran Mau-Them 2019 PMID 30166628)

SS Ray 2022 - PMID: 36476864 - strong support for dominant negative - evidence that abnormal product co-assembles with WT

• In vitro human model, patient fibroblast cell lines. Western blot showed only a small or no reduction of IRF2BPL protein levels compared w/ healthy controls (used an antibody that only detects full length protein and not the truncated version). Generated induced neurons using patient cells and found that the protein mainly localized in the nucleus with faint cytoplasmic signal. Controls had exclusive nuclear localization.

• Then generated induced neuronal progenitory cells that were then differentiated into astrocytes. All patients exhibited an activiated phenotype with altered morphology and higher GFAP expression compared with controls. Cellular localization showed full length protein was mislocalized to cytoplasm in the form of smears or aggregates.

• Truncated protein was found to dimerize and mis-localize full length IRF2BPL - transfected HEK293 cells, a pull-down assay showed the IRF2BPL protein can dimerize with itself and that truncated isoforms are stable. Full length protein was redistributed to the cytoplasm in the form of aggregates when expressed with truncated protein forms.

• Co-culture assays of mouse neurons on a monolayer of healthy or patient induced astrocytes - found that patient cocultures had lower rates of survival. Treatment with a CuATSM drug improved neuronal survival, but did not rescue mislocalization in patient induced astrocytes.

• Patient derived induced astrocytes showed abberant mito respiration which was rescued by CuATSM

Tran Mau-Them 2019 PMID 30166628 - NOT supportive of LOF

• RNA analysis on patient derived fibroblasts confirmed that the truncations escaped NMD with a ratio of at least 1:1 with the WT allele, suggesting that the shorter proten might be translated (fig 1C)

Marcogliese 2022 PMID: 35044823 - supports a potential pathway, but suggests LOF may be mechanism.

• Overexpression of human IRF2BPL and Drosophila Pits in the fly wing imaginal disc causes a phenotype that has been seen with loss of Wnt signaling.

• Zebrafish lacking irf2bpl display neurobehavioral defects - homozygous mutants were viable, fertile, and morphologically similar to WT and het siblings. At 5 d.p.f. they showed lower total activity, at 7 d.p.f. reduced locomootor activity, lower startle response. wnt1 transcription were increased in mutant animals compared to wt siblings. Not a good model because the fish were homozygous, and human disease is dominant.

• Patient fibroblasts induced into astrocytes showed increased WNT1 mRNA and protein expression. indicates that NEDAMSS-associated truncations inhibit the negative regulation of WNT1 by IRF2BPL.

Reviewed variants in ClinVar to try to find LOF citations; the only ones I coudl find cite the papers described above, and in fact I found conflicting statements about LOF in two different RGP variants. Yet they both applied PVS1. Variation ID 1691661 NCBI - WWW Error Blocked Diagnostic and 986391 NCBI - WWW Error Blocked Diagnostic

Also looked for guidance on how to curate single exon genes on ClinGen website, and couldn’t find any helpful info.

Penetrance

(list source/PMID)

Source:

Age of Onset

(list source/PMID)

Severity

Clinical Features

Typically normal early development, then motor and language regression.

Abnormal movements - ataxia / dystonia

Seizures

Less common:

• Dysmorphic features

• Poor vision nystagmus, exotropia, high myopia, retinal hyper and hypopigmentation, abnormal ERG.

• expanding phenotype

• Shelkowitz 2019 PMID: 31432588 - expanding phenotype - hypertrophic cardiomayopathy, gastrointestinal issues, poor vision with nystagmus, exotropia, high myopia, retinal hyper and hypopigmentation, abnormal ERG.

• Horovitz 2023 37346291 - dysmorphic features, global developmental delay, dysmorphic features,

• Sources:

HPO Terms

https://hpo.jax.org/app/

Gene SOPs & Notes

The mechanism is unknown, but it is likely LOF or dominant negative with many truncating variants reported across the gene. For truncating variants whose stop is located between p.119 to 769, apply PM4_Strong. See example summary sentences in Accession ID E3720134684

Curation Summary

The IRF2BPL gene is associated with autosomal dominant neurodevelopmental disorder with regression, abnormal movements, loss of speech, and seizures. It is typically characterized by normal development followed by regression of motor skills and speech, seizures, and abnormal movements such as ataxia and dystonia (PMID: 30057031, 30166628, 37346291, 36476864). Additional features have also been described, including dysmorphic features, developmental delay, and poor vision (PMID: 37346291, 31432588)

Case ID, Curator name, Date, Jira ticket link

Andrea Oza 12.28.2023 Accession ID E3720134684