Is NONO p.Pro82fs (c.245del) pathogenic?

NONO p.Pro82fs (c.245del) is classified Pathogenic in NONO (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-11). No gnomAD frequency available for this variant.

How common is NONO p.Pro82fs (c.245del) in the general population?

NONO p.Pro82fs (c.245del) is no gnomAD frequency available for this variant (gnomAD).

NONO p.Pro82fs

c.245del · rs1602386427 · VCV647910

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 in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -0.22, 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: NONO
Protein: p.Pro82fs
Coding: c.245del
MANE Select: NM_007363
dbSNP: rs1602386427
Type: Deletion
Location: chrX:71291868 (GRCh38)
Structure: AlphaFold pLDDT 77.76 · 9 PDB
Residue 82: the rrm 1 domain; the 'dbhs' region

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

Similar variants

NONO c.322_348+280del Likely pathogenic ★ same type
NONO c.332_348+280del Likely pathogenic ★ same type
NONO c.348+2_348+15del Pathogenic ★ same type
NONO p.Ala100fs Pathogenic ★ same type
NONO p.Asn397fs Likely pathogenic ★ same type
NONO p.Gly415fs Likely pathogenic ★ same type
NONO p.Lys92fs Likely pathogenic ★ same type
NONO p.Phe77fs 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/nono-p-pro82fs (accessed [today's date]).

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