DIP2B p.Leu48=
c.144C>T · rs146296554 · VCV731362
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.86%, eas)
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 -0.65 | GERP -3.3, phastCons 0.012 |
| Overall | ||
| CADD | 4.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.86%
East Asian · 833/44,866 alleles
Filtering AF
1.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.71%
Overall
0.057%
920/1,614,138 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.86% | 54 |
| Remaining individualsnot grpmax-eligible | 0.0976% | 1,025 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.011% | 9,108 |
| Admixed American | 0.00333% | 30,004 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
| European (non-Finnish) | 0.000932% | 107,274 |
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.Leu48=
- Coding
- c.144C>T
- MANE Select
- NM_173602
- dbSNP
- rs146296554
- Type
- single nucleotide variant
- Location
- chr12:50626019 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.83
- Residue 48
- the dmap1-binding domain; 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-leu48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown