Is NBEA p.Ser32Asn (c.95_96delinsAT) pathogenic?

NBEA p.Ser32Asn (c.9596delinsAT) is classified Uncertain significance in NBEA (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-30). Absent from gnomAD; Associated with neurodevelopmental disorder with or without early-onset generalized epilepsy.

What condition is associated with NBEA p.Ser32Asn (c.95_96delinsAT)?

NBEA p.Ser32Asn (c.95_96delinsAT) is associated with neurodevelopmental disorder with or without early-onset generalized epilepsy (ClinVar).

How common is NBEA p.Ser32Asn (c.95_96delinsAT) in the general population?

NBEA p.Ser32Asn (c.95_96delinsAT) is absent from gnomAD (gnomAD).

NBEA p.Ser32Asn

c.95_96delinsAT · rs2500554387 · VCV2434049

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder with or without early-onset generalized epilepsy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.71	GERP 0.91, phastCons 0.26
Regional constraint	o/e 1.34	unconstrained · MANE · 171 bp · p 0.0012 · regional, not allelic
Region caveats
Repeat context	tandem	(CGG)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NBEA
Protein: p.Ser32Asn
Coding: c.95_96delinsAT
MANE Select: NM_001385012
dbSNP: rs2500554387
Type: Indel
Location: chr13:34942915 (GRCh38)
Gene constraint: LOEUF 0.137 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

Full NBEA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder with or without early-onset generalized epilepsy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NBEA p.Leu2771Phe Uncertain significance ★ same condition
NBEA p.Arg1299Ter Pathogenic/Likely pathogenic ★★ same condition
NBEA p.Arg1493fs Pathogenic ★★ same condition
NBEA p.Arg2866Ter Pathogenic ★★ same condition
NBEA p.Arg696Ter Pathogenic/Likely pathogenic ★★ same condition
NBEA p.Asn1121fs Likely pathogenic ★★ same condition
NBEA p.Ala603Val Uncertain significance ★★ same condition
NBEA p.Asn1141Asp Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nbea-p-ser32asn (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown