DIP2B p.Cys753=
c.2259T>C · rs148495455 · VCV736531
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.33%, 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 0.68 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 9.154 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.33%
South Asian · 1,211/91,086 alleles
Filtering AF
1.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.0803%
1,296/1,614,178 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.33% | 75 |
| Remaining individualsnot grpmax-eligible | 0.0864% | 1,157 |
| Middle Eastern | 0.066% | 1,516 |
| African / African-American | 0.00666% | 15,010 |
| East Asian | 0.00223% | 44,882 |
| European (non-Finnish) | 0.00169% | 59,001 |
| Admixed American | 0.00167% | 60,024 |
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.Cys753=
- Coding
- c.2259T>C
- MANE Select
- NM_173602
- dbSNP
- rs148495455
- Type
- single nucleotide variant
- Location
- chr12:50699136 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.83
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-cys753 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown