DIP2B p.Ile179=
c.537T>A · VCV3910961
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0623%, nfe)
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 2.3 | GERP 0.28, phastCons 1 |
| Overall | ||
| CADD | 9.812 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0623%
European (non-Finnish) · 735/1,180,040 alleles
Filtering AF
0.0585%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.057%
Overall
0.0465%
751/1,614,060 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0623% | 1,605 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| African / African-American | 0.00667% | 14,983 |
| Admixed American | 0.00167% | 59,990 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
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
- DIP2B
- Protein
- p.Ile179=
- Coding
- c.537T>A
- MANE Select
- NM_173602
- Type
- single nucleotide variant
- Location
- chr12:50671295 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.83
- Residue 179
- the 'disordered' region
Similar variants
- DIP2B p.Asp501Val Uncertain significance ★★ ⚠ same type
- DIP2B p.Cys1071Ser Uncertain significance ★★ ⚠ same type
- DIP2B p.His1027Arg Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile681Val Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile968Thr Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile994Leu Uncertain significance ★★ ⚠ same type
- DIP2B p.Pro244Ala Uncertain significance ★★ ⚠ same type
- DIP2B p.Pro513Ser 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/dip2b-p-ile179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown