Is ADNP p.Val180fs (c.539_542del) pathogenic?

ADNP p.Val180fs (c.539542del) is classified Pathogenic in ADNP (ClinVar, Multiple submitters, 12 submitters; last evaluated 2024-02-01). Absent from gnomAD; Associated with ADNP-related disorder.

What condition is associated with ADNP p.Val180fs (c.539_542del)?

ADNP p.Val180fs (c.539_542del) is associated with ADNP-related disorder, ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (ClinVar).

How common is ADNP p.Val180fs (c.539_542del) in the general population?

ADNP p.Val180fs (c.539_542del) is absent from gnomAD (gnomAD).

ADNP p.Val180fs

c.539_542del · rs1057518345 · VCV373314

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ADNP-related 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 3.3	GERP 1.7, 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: ADNP
Protein: p.Val180fs
Coding: c.539_542del
MANE Select: NM_001282531
dbSNP: rs1057518345
Type: Deletion
Location: chr20:50894172 (GRCh38)
Gene constraint: LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 57.07

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

Disease context

ADNP-related disorder

Also linked: ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder

Similar variants

ADNP p.Leu831fs Pathogenic/Likely pathogenic ★★ same condition
ADNP p.Lys773fs Pathogenic ★★ same condition
ADNP p.Lys829fs Pathogenic/Likely pathogenic ★★ same condition
ADNP p.Ser769fs Pathogenic/Likely pathogenic ★★ same condition
ADNP p.Ser955fs Pathogenic/Likely pathogenic ★★ same condition
ADNP p.Thr718_Tyr719insTer Pathogenic ★★ same condition
ADNP c.202-5_202-1del Likely pathogenic ★ same condition
ADNP p.Arg730fs 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-val180fs (accessed [today's date]).

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