DIPK2B p.Ser340=
c.1020C>T · rs752948825 · VCV3049454
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0459%, mid)
Conditions
1
DIPK2B-related disorder
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 -1 | GERP -3.4 |
| Overall | ||
| CADD | 0.507 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0459%
Middle Eastern · 2/4,360 alleles
Filtering AF
0.00811%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00406%
Overall
0.00425%
51/1,199,147 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0459% | 2,180 |
| African / African-American | 0.0122% | 8,173 |
| East Asian | 0.00902% | 11,087 |
| Admixed American | 0.00678% | 14,754 |
| European (non-Finnish) | 0.00394% | 25,404 |
| Remaining individualsnot grpmax-eligible | 0.00212% | 47,128 |
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
- DIPK2B
- Protein
- p.Ser340=
- Coding
- c.1020C>T
- MANE Select
- NM_176819
- dbSNP
- rs752948825
- Type
- single nucleotide variant
- Location
- chrX:45151934 (GRCh38)
- Structure
- AlphaFold pLDDT 84.17
Disease context
DIPK2B-related disorder
Similar variants
- DIPK2B p.Gly231Arg Uncertain significance ⚠ same condition
- DIPK2B p.Arg128Lys Benign same condition
- DIPK2B p.Arg143Leu Benign same condition
- DIPK2B p.Asp391His Likely benign ⚠ same condition
- DIPK2B p.Leu366= Likely benign same condition
- DIPK2B p.Ser105Pro Benign ⚠ same condition
- DIPK2B p.Ala133Glu Benign ★★ same type
- DIPK2B p.Lys364= 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/dipk2b-p-ser340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown