CD99L2 p.Arg169Gln
c.506G>A · rs143706982 · VCV2342255
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0832 | likely benign |
|---|---|---|
| REVEL | 0.015 | strongly benign-leaning |
| SaProt | LLR -7.59 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.98 | GERP -1.9 |
| Regional constraint | o/e 1.15 | unconstrained · MANE · 130 kb · p 0.025 · regional, not allelic |
| Overall | ||
| CADD | 2.58 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.0728% | 1,374 |
| Middle Easterngrpmax | 0.046% | 2,173 |
| East Asian | 0.0178% | 5,627 |
| Admixed American | 0.0175% | 5,710 |
| South Asian | 0.0106% | 9,448 |
| African / African-American | 0.0105% | 9,559 |
| Remaining individualsnot grpmax-eligible | 0.00841% | 11,897 |
| Finnishnot grpmax-eligible | 0.00645% | 15,510 |
| European (non-Finnish) | 0.00492% | 20,342 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- CD99L2
- Protein
- p.Arg169Gln
- Coding
- c.506G>A
- MANE Select
- NM_031462
- dbSNP
- rs143706982
- Type
- single nucleotide variant
- Location
- chrX:150777473 (GRCh38)
- Structure
- AlphaFold pLDDT 55.71
- Residue 169
- the 'disordered' region
Similar variants
- CD99L2 p.Arg169Trp Uncertain significance ★ ⚠ same residue
- CD99L2 p.Asp175Asn Benign/Likely benign ★★ ⚠ same type
- CD99L2 c.203-9C>A Uncertain significance ★ same type
- CD99L2 c.68-5755G>T Uncertain significance ★ same type
- CD99L2 p.Ala182Ser Uncertain significance ★ ⚠ same type
- CD99L2 p.Arg104Lys Uncertain significance ★ ⚠ same type
- CD99L2 p.Arg131Gln Uncertain significance ★ ⚠ same type
- CD99L2 p.Arg135Cys 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/cd99l2-p-arg169gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown