Is NONO p.Lys68fs (c.201_202dup) pathogenic?

NONO p.Lys68fs (c.201202dup) is classified Pathogenic in NONO (ClinVar, Single submitter, 1 submitter). No gnomAD frequency available for this variant; Associated with syndromic X-linked intellectual disability 34.

What condition is associated with NONO p.Lys68fs (c.201_202dup)?

NONO p.Lys68fs (c.201_202dup) is associated with syndromic X-linked intellectual disability 34 (ClinVar).

How common is NONO p.Lys68fs (c.201_202dup) in the general population?

NONO p.Lys68fs (c.201_202dup) is no gnomAD frequency available for this variant (gnomAD).

NONO p.Lys68fs

c.201_202dup · rs2148033408 · VCV1700215

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

Conditions

syndromic X-linked intellectual disability 34

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 9.7	GERP 1, 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.Lys68fs
Coding: c.201_202dup
MANE Select: NM_007363
dbSNP: rs2148033408
Type: Microsatellite
Location: chrX:71291820 (GRCh38)
Structure: AlphaFold pLDDT 77.76 · 9 PDB
Residue 68: the 'dbhs' region

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

Disease context

syndromic X-linked intellectual disability 34 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NONO p.His106fs Likely pathogenic ★ same condition
NONO p.Ala439dup Conflicting classifications of pathogenicity ★ same condition
NONO p.Gln35_Pro36insGln Uncertain significance ★ same condition
NONO p.Lys68Asn Uncertain significance ★ ⚠ same residue
NONO c.154+1GT[2] Pathogenic same condition
NONO c.651-1G>C Likely pathogenic ★★ same condition
NONO p.Ala377= Pathogenic ★★ same condition
NONO p.Arg184Ter 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/nono-p-lys68fs (accessed [today's date]).

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