ADNP p.Phe770=
c.2310T>C · rs189595164 · VCV747523
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.307%, eas)
Conditions
2
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 2.1 | GERP -0.53, phastCons 1 |
| Overall | ||
| CADD | 7.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.307%
East Asian · 138/44,884 alleles
Filtering AF
0.266%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.25%
Overall
0.0129%
208/1,614,190 alleles · rare
exomes 175/1,461,888 · genomes 33/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.307% | 325 |
| Remaining individualsnot grpmax-eligible | 0.0576% | 1,736 |
| African / African-American | 0.0173% | 5,771 |
| Admixed American | 0.00833% | 12,006 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.000847% | 118,004 |
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.Phe770=
- Coding
- c.2310T>C
- MANE Select
- NM_001282531
- dbSNP
- rs189595164
- Type
- single nucleotide variant
- Location
- chr20:50892404 (GRCh38)
- Gene constraint
- LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.07
- Residue 770
- a DNA-binding region
Similar variants
- ADNP p.Phe770Leu Uncertain significance ★ ⚠ same residue
- ADNP p.Arg173Ter Pathogenic ★★ same condition
- ADNP p.Arg225Ter Pathogenic/Likely pathogenic ★★ same condition
- ADNP p.Arg730Ter Pathogenic/Likely pathogenic ★★ same condition
- ADNP p.Ser738Ter Pathogenic ★★ same condition
- ADNP p.Trp446Ter Pathogenic ★★ same condition
- ADNP p.Tyr172Ter Likely pathogenic ★★ same condition
- ADNP p.Tyr378Ter 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-phe770 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown