DIPK2B p.Leu366=
c.1096C>T · rs201256036 · VCV3050838
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.459%, afr)
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 4.2 | GERP -0.25, phastCons 1 |
| Overall | ||
| CADD | 6.818 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.459%
African / African-American · 264/57,475 alleles
Filtering AF
0.414%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.396%
Overall
0.0239%
289/1,209,973 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.459% | 218 |
| Remaining individualsnot grpmax-eligible | 0.0357% | 2,800 |
| Middle Eastern | 0.023% | 4,354 |
| Admixed American | 0.0109% | 9,170 |
| European (non-Finnish) | 0.000224% | 447,409 |
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.Leu366=
- Coding
- c.1096C>T
- MANE Select
- NM_176819
- dbSNP
- rs201256036
- Type
- single nucleotide variant
- Location
- chrX:45151858 (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.Ser105Pro Benign ⚠ same condition
- DIPK2B p.Ser340= Likely 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-leu366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown