Is ADNP p.Glu1024fs (c.3071_3072del) pathogenic?

ADNP p.Glu1024fs (c.30713072del) is classified Uncertain significance in ADNP (ClinVar, Single submitter, 1 submitter). Associated with ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder.

ADNP p.Glu1024fs

Q: What condition is associated with ADNP p.Glu1024fs (c.3071_3072del)?

ADNP p.Glu1024fs (c.3071_3072del) is associated with ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (ClinVar).

c.3071_3072del · VCV3383133

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder

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	escapes	premature termination codon in the last exon (6 of 6) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 10	GERP 1.9, phastCons 1

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

Variant & gene context

Gene: ADNP
Protein: p.Glu1024fs
Coding: c.3071_3072del
MANE Select: NM_001282531
Type: Microsatellite
Location: chr20:50891642 (GRCh38)
Gene constraint: LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 57.07
Residue 1024: the 'disordered' region

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

Disease context

ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ADNP p.Asn832fs Pathogenic ★★ same condition
ADNP p.Glu218_Ser219insTer Pathogenic ★★ same condition
ADNP p.Asp735del Uncertain significance ★★ same condition
ADNP p.Glu1024Val Uncertain significance ★★ ⚠ same residue
ADNP p.Lys279del Benign/Likely benign ★★ same condition
ADNP p.Arg646fs Pathogenic ★ same condition
ADNP p.Asp277fs Likely pathogenic ★ same condition
ADNP p.Lys777fs Likely 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/adnp-p-glu1024fs (accessed [today's date]).

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