DIP2C p.Ala589=
c.1767G>A · VCV3715069
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00447%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.017 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.38 | GERP -3.7, phastCons 0.002 |
| Overall | ||
| CADD | 1.235 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00447%
East Asian · 2/44,762 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000496%
Overall
0.00118%
19/1,609,610 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00447% | 22,381 |
| African / African-American | 0.00402% | 24,889 |
| South Asian | 0.00223% | 44,906 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,348 |
| European (non-Finnish) | 0.000933% | 107,189 |
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
- DIP2C
- Protein
- p.Ala589=
- Coding
- c.1767G>A
- MANE Select
- NM_014974
- Type
- single nucleotide variant
- Location
- chr10:384136 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.64
Similar variants
- DIP2C p.Ala1066Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1066Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1101Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1155Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1466Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala193Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala422Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala71Thr 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/dip2c-p-ala589 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown