DISP3 p.Ser861=
c.2583G>A · rs375072553 · VCV3057940
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0417%, amr)
Conditions
1
DISP3-related disorder
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 0.6 | GERP -3.4, phastCons 0.75 |
| Overall | ||
| CADD | 5.418 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0417%
Admixed American · 25/59,984 alleles
Filtering AF
0.0306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0295%
Overall
0.0276%
446/1,613,764 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0417% | 2,399 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,975 |
| European (non-Finnish) | 0.0334% | 2,995 |
| East Asian | 0.00446% | 22,441 |
| African / African-American | 0.004% | 24,972 |
| South Asian | 0.0011% | 91,086 |
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
- DISP3
- Protein
- p.Ser861=
- Coding
- c.2583G>A
- MANE Select
- NM_020780
- dbSNP
- rs375072553
- Type
- single nucleotide variant
- Location
- chr1:11525282 (GRCh38)
- Gene constraint
- LOEUF 0.886 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.84
Disease context
DISP3-related disorder
Similar variants
- DISP3 c.1749+5G>A Likely benign same condition
- DISP3 c.3230-4G>A Likely benign same condition
- DISP3 p.Ala1000= Likely benign same condition
- DISP3 p.Ala1297= Benign same condition
- DISP3 p.Ala650Thr Benign same condition
- DISP3 p.Arg1022His Likely benign same condition
- DISP3 p.Arg166Gln Likely benign same condition
- DISP3 p.Arg294= Likely benign 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/disp3-p-ser861 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown