DISP1 p.Pro396=
c.1188A>G · rs200646799 · VCV788772
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, amr)
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 -7 | |
| Overall | ||
| CADD | 0.179 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Admixed American · 20/60,022 alleles
Filtering AF
0.0221%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0193%
Overall
0.0186%
301/1,614,228 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0333% | 3,001 |
| European (non-Finnish) | 0.0225% | 4,453 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| African / African-American | 0.00266% | 37,531 |
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
- DISP1
- Protein
- p.Pro396=
- Coding
- c.1188A>G
- MANE Select
- NM_001377229
- dbSNP
- rs200646799
- Type
- single nucleotide variant
- Location
- chr1:223002585 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.21 · 4 PDB
- Residue 396
- a UniProt-annotated variant site (in hpe10; uncertain significance; heterozygous variant inherited from unaffected parent)
Similar variants
- DISP1 p.Ala1123Thr Uncertain significance ★★ ⚠ same type
- DISP1 p.Ala1204Thr Uncertain significance ★★ ⚠ same type
- DISP1 p.Ala248Val Uncertain significance ★★ ⚠ same type
- DISP1 p.Ala733Val Uncertain significance ★★ ⚠ same type
- DISP1 p.Arg1061His Uncertain significance ★★ ⚠ same type
- DISP1 p.Arg718His Uncertain significance ★★ ⚠ same type
- DISP1 p.Arg763His Uncertain significance ★★ ⚠ same type
- DISP1 p.Asn1035Ser Uncertain significance ★★ ⚠ 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/disp1-p-pro396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown