ADNP p.Val751del
c.2248GTT[1] · rs748645628 · VCV1976540
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP -0.41, phastCons 1 |
| Overall | ||
| CADD | 18.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,912 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000867%
14/1,614,032 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.004% | 24,971 |
| South Asian | 0.0022% | 45,541 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| Finnishnot grpmax-eligible | 0.00156% | 64,042 |
| European (non-Finnish) | 0.000593% | 168,577 |
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.Val751del
- Coding
- c.2248GTT[1]
- MANE Select
- NM_001282531
- dbSNP
- rs748645628
- Type
- Microsatellite
- Location
- chr20:50892461 (GRCh38)
- Gene constraint
- LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.07
Similar variants
- ADNP p.Val751fs Likely pathogenic same residue
- ADNP p.Asn832fs Pathogenic ★★ same type
- ADNP p.Glu218_Ser219insTer Pathogenic ★★ same type
- ADNP p.Val19fs Pathogenic ★★ same type
- ADNP p.Asp735del Uncertain significance ★★ same type
- ADNP p.Val963del Uncertain significance ★★ same type
- ADNP p.Lys279del Benign/Likely benign ★★ same type
- ADNP p.Arg646fs 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-val751del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown