DCPS p.Ala80=
c.240C>T · rs144876585 · VCV2642531
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0836%, sas)
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 -4 | GERP -5.5 |
| Overall | ||
| CADD | 6.456 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0836%
South Asian · 76/90,926 alleles
Filtering AF
0.0685%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0629%
Overall
0.0146%
235/1,612,502 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0836% | 1,196 |
| Middle Eastern | 0.0502% | 1,993 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,161 |
| European (non-Finnish) | 0.0115% | 8,669 |
| African / African-American | 0.00401% | 24,953 |
| East Asian | 0.00223% | 44,828 |
| Finnishnot grpmax-eligible | 0.00156% | 63,996 |
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
- DCPS
- Protein
- p.Ala80=
- Coding
- c.240C>T
- MANE Select
- NM_014026
- dbSNP
- rs144876585
- Type
- single nucleotide variant
- Location
- chr11:126306608 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.18 · 11 PDB
- Residue 80
- a β-strand
Similar variants
- DCPS p.Arg152Ter Likely pathogenic ★★ same type
- DCPS p.Ala184Thr Uncertain significance ★★ ⚠ same type
- DCPS p.Arg145Cys Uncertain significance ★★ ⚠ same type
- DCPS p.Arg242Gly Uncertain significance ★★ ⚠ same type
- DCPS p.Pro235Leu Uncertain significance ★★ ⚠ same type
- DCPS p.Ala186= Benign/Likely benign ★★ same type
- DCPS p.Asp324= Likely benign ★★ same type
- DCPS p.Gln105= Benign ★★ 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/dcps-p-ala80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown