ADNP p.Asn459=
c.1377T>C · rs149976600 · VCV1771198
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0733%, afr)
Conditions
1
Inborn genetic diseases
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 0.17 | GERP 0.65, phastCons 0.25 |
| Overall | ||
| CADD | 5.581 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0733%
African / African-American · 55/75,018 alleles
Filtering AF
0.0578%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0522%
Overall
0.00372%
60/1,614,140 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0733% | 1,364 |
| Admixed American | 0.00167% | 60,022 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
| European (non-Finnish) | 0.000254% | 393,340 |
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.Asn459=
- Coding
- c.1377T>C
- MANE Select
- NM_001282531
- dbSNP
- rs149976600
- Type
- single nucleotide variant
- Location
- chr20:50893337 (GRCh38)
- Gene constraint
- LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.07
Similar variants
- ADNP p.Ser738Ter Pathogenic ★★ same condition
- ADNP p.Trp446Ter Pathogenic ★★ same condition
- ADNP p.Arg264Gln Uncertain significance ★★ ⚠ same condition
- ADNP p.Arg296Gln Uncertain significance ★★ ⚠ same condition
- ADNP p.Asn331Tyr Uncertain significance ★★ ⚠ same condition
- ADNP p.Asn951Ser Uncertain significance ★★ ⚠ same condition
- ADNP p.Gln302His Uncertain significance ★★ ⚠ same condition
- ADNP p.Glu1024Val Uncertain significance ★★ ⚠ 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-asn459 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown