Is NBAS p.Arg1368fs (c.4104_4105del) pathogenic?

NBAS p.Arg1368fs (c.41044105del) is classified Pathogenic in NBAS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-12). No gnomAD frequency available for this variant.

How common is NBAS p.Arg1368fs (c.4104_4105del) in the general population?

NBAS p.Arg1368fs (c.4104_4105del) is no gnomAD frequency available for this variant (gnomAD).

NBAS p.Arg1368fs

c.4104_4105del · rs2528567165 · VCV2827869

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 35 of 52
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.8, 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.Arg1368fs
Coding: c.4104_4105del
MANE Select: NM_015909
dbSNP: rs2528567165
Type: Microsatellite
Location: chr2:15352066 (GRCh38)
Gene constraint: LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.42
Residue 1368: a UniProt-annotated variant site (in ilfs2; uncertain significance); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance; reduced protein expression levels in fibroblasts); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance; reduced collagen secretion; diffuse collagen bundles; reduced protein expression in fibroblasts); the 'interaction with zw10 and rint1' region

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

Similar variants

NBAS p.Arg1368Gly Uncertain significance ★ ⚠ same residue
NBAS p.Val1613fs Pathogenic/Likely pathogenic ★★ same type
NBAS c.5390-17_5390-14del Benign/Likely benign ★★ same type
NBAS p.Glu1028fs Likely pathogenic ★ same type
NBAS p.Leu1846fs Pathogenic ★ same type
NBAS p.Leu901fs Pathogenic ★ same type
NBAS p.Val109fs Pathogenic ★ same type
NBAS p.Glu466del Uncertain significance ★ 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-arg1368fs (accessed [today's date]).

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