DIPK2B p.Lys364=
c.1092G>A · rs142916210 · VCV711138
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.35%, afr)
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 -0.024 | GERP -0.18, phastCons 0.024 |
| Overall | ||
| CADD | 5.532 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.35%
African / African-American · 777/57,498 alleles
Filtering AF
1.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.0788%
953/1,210,112 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.35% | 74 |
| Middle Eastern | 0.23% | 435 |
| Remaining individualsnot grpmax-eligible | 0.0861% | 1,161 |
| Admixed American | 0.0589% | 1,699 |
| European (non-Finnish) | 0.0106% | 9,420 |
| South Asian | 0.00353% | 28,345 |
| East Asian | 0.00296% | 33,756 |
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.Lys364=
- Coding
- c.1092G>A
- MANE Select
- NM_176819
- dbSNP
- rs142916210
- Type
- single nucleotide variant
- Location
- chrX:45151862 (GRCh38)
- Structure
- AlphaFold pLDDT 84.17
Similar variants
- DIPK2B p.Ala133Glu Benign ★★ same type
- DIPK2B p.Thr138Ser Uncertain significance ★ ⚠ same type
- DIPK2B c.499-4G>T Likely benign ★ same type
- DIPK2B c.499-7C>T Likely benign ★ same type
- DIPK2B p.Ala328= Likely benign ★ same type
- DIPK2B p.Arg45= Likely benign ★ same type
- DIPK2B p.Ile225= Likely benign ★ same type
- DIPK2B p.Lys70Asn 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-lys364 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown