CD99L2 p.Ser244=
c.732C>T · rs199773498 · VCV2661638
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.026%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.3 | GERP -2.8 |
| Overall | ||
| CADD | 0.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.026%
African / African-American · 14/53,838 alleles
Filtering AF
0.0156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0125%
Overall
0.00129%
15/1,161,636 alleles · ultra-rare
exomes 9/1,048,814 · genomes 6/112,822 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.026% | 3,846 |
| Remaining individualsnot grpmax-eligible | 0.00219% | 45,597 |
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.Ser244=
- Coding
- c.732C>T
- MANE Select
- NM_031462
- dbSNP
- rs199773498
- Type
- single nucleotide variant
- Location
- chrX:150769091 (GRCh38)
- Structure
- AlphaFold pLDDT 55.71
Similar variants
- 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
- CD99L2 p.Arg169Gln 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-ser244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown