Is NBAS p.Pro454fs (c.1359_1366del) pathogenic?

NBAS p.Pro454fs (c.13591366del) is classified Pathogenic in NBAS (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-02). No gnomAD frequency available for this variant.

How common is NBAS p.Pro454fs (c.1359_1366del) in the general population?

NBAS p.Pro454fs (c.1359_1366del) is no gnomAD frequency available for this variant (gnomAD).

NBAS p.Pro454fs

c.1359_1366del · rs2528139805 · VCV2101614

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 15 of 52
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	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.Pro454fs
Coding: c.1359_1366del
MANE Select: NM_015909
dbSNP: rs2528139805
Type: Deletion
Location: chr2:15474300 (GRCh38)
Gene constraint: LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.42
Residue 454: 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

Similar variants

NBAS p.Pro454Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
NBAS p.Asp2149_Ile2150insTer Pathogenic/Likely pathogenic ★★ same type
NBAS p.Cys1112fs Pathogenic ★★ same type
NBAS p.Gln2232fs Pathogenic/Likely pathogenic ★★ same type
NBAS p.Gln44fs Pathogenic/Likely pathogenic ★★ same type
NBAS p.Glu1092fs Pathogenic/Likely pathogenic ★★ same type
NBAS p.Ile984fs Pathogenic/Likely pathogenic ★★ same type
NBAS p.Leu1507fs Pathogenic/Likely pathogenic ★★ same type

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-pro454fs (accessed [today's date]).

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