ADNP p.Ser1032=
c.3096C>T · VCV3628084
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00958%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00958%
European (non-Finnish) · 113/1,180,042 alleles
Filtering AF
0.00809%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0076%
Overall
0.0075%
121/1,613,902 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00958% | 10,443 |
| African / African-American | 0.00534% | 18,726 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| Admixed American | 0.00167% | 60,000 |
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.Ser1032=
- Coding
- c.3096C>T
- MANE Select
- NM_001282531
- Type
- single nucleotide variant
- Location
- chr20:50891618 (GRCh38)
- Gene constraint
- LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.07
Similar variants
- ADNP p.Ser1032Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
- ADNP p.Arg173Ter Pathogenic ★★ same type
- ADNP p.Arg216Ter Pathogenic ★★ same type
- ADNP p.Arg225Ter Pathogenic/Likely pathogenic ★★ same type
- ADNP p.Arg306Ter Pathogenic/Likely pathogenic ★★ same type
- ADNP p.Arg730Ter Pathogenic/Likely pathogenic ★★ same type
- ADNP p.Ser738Ter Pathogenic ★★ same type
- ADNP p.Trp446Ter 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/adnp-p-ser1032 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown