Is NBAS p.Lys298fs (c.893del) pathogenic?

NBAS p.Lys298fs (c.893del) is classified Likely pathogenic in NBAS (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD; Associated with infantile liver failure syndrome 2.

What condition is associated with NBAS p.Lys298fs (c.893del)?

NBAS p.Lys298fs (c.893del) is associated with infantile liver failure syndrome 2 (ClinVar).

How common is NBAS p.Lys298fs (c.893del) in the general population?

NBAS p.Lys298fs (c.893del) is absent from gnomAD (gnomAD).

NBAS p.Lys298fs

Q: How is Fever-associated acute infantile liver failure syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.893del · rs2148636494 · VCV1328385

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

infantile liver failure syndrome 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 11 of 52
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: NBAS
Protein: p.Lys298fs
Coding: c.893del
MANE Select: NM_015909
dbSNP: rs2148636494
Type: Deletion
Location: chr2:15504206 (GRCh38)
Gene constraint: LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.42
Residue 298: a UniProt-annotated variant site (in ilfs2; uncertain significance); the 'interaction with use1' region

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

Disease context

infantile liver failure syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Fever-associated acute infantile liver failure syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

NBAS p.Asp2149_Ile2150insTer Pathogenic/Likely pathogenic ★★ same condition
NBAS p.Ile984fs Pathogenic/Likely pathogenic ★★ same condition
NBAS p.Leu1726fs Pathogenic/Likely pathogenic ★★ same condition
NBAS p.Ser1419fs Pathogenic ★★ same condition
NBAS c.4657_4659+18del Likely pathogenic ★ same condition
NBAS p.Ala1686fs Likely pathogenic ★ same condition
NBAS p.Lys1169fs Likely pathogenic ★ same condition
NBAS p.Phe1754fs Pathogenic ★ 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/nbas-p-lys298fs (accessed [today's date]).

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