ADNP p.Arg1023fs
c.3069_3072del · rs1279657093 · VCV988372
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 |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed Americangrpmax | 0.00333% | 30,003 |
| Finnishnot grpmax-eligible | 0.00156% | 63,986 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000678% | 147,506 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ADNP
- Protein
- p.Arg1023fs
- Coding
- c.3069_3072del
- MANE Select
- NM_001282531
- dbSNP
- rs1279657093
- 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 1023
- the 'disordered' region
Disease context
Similar variants
- ADNP p.Gln414fs Pathogenic ★ same condition
- ADNP p.Leu682fs Likely pathogenic ★ same condition
- ADNP p.Arg1023Lys Uncertain significance ★ ⚠ same residue
- ADNP p.Arg306Ter Pathogenic/Likely pathogenic ★★ same condition
- ADNP p.Arg730Ter Pathogenic/Likely pathogenic ★★ same condition
- ADNP p.Ile22fs Pathogenic/Likely pathogenic ★★ same condition
- ADNP p.Ser769fs Pathogenic/Likely pathogenic ★★ same condition
- ADNP p.Thr718_Tyr719insTer 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-arg1023fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown