DISP1 p.Pro25=
c.75G>A · rs61746477 · VCV439599
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 17.9%, sas) — too common for a highly-penetrant pathogenic allele
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 -3.5 | GERP -4.2 |
| Overall | ||
| CADD | 4.529 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
17.9%
South Asian · 16,343/91,068 alleles
Filtering AF
17.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.6%
Overall
9.21%
148,690/1,613,938 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 17.9% | 6 |
| Admixed American | 12.5% | 8 |
| East Asian | 11.5% | 9 |
| Finnishnot grpmax-eligible | 10.4% | 10 |
| Remaining individualsnot grpmax-eligible | 9.65% | 10 |
| European (non-Finnish) | 8.33% | 12 |
| African / African-American | 8.32% | 12 |
| Middle Eastern | 7.21% | 14 |
| Ashkenazi Jewishnot grpmax-eligible | 6.81% | 15 |
| Amishnot grpmax-eligible | 4.61% | 22 |
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.Pro25=
- Coding
- c.75G>A
- MANE Select
- NM_001377229
- dbSNP
- rs61746477
- Type
- single nucleotide variant
- Location
- chr1:222942898 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.21 · 4 PDB
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-pro25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown