CD99L2 p.Pro253=
c.759G>A · rs138311396 · VCV746998
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.273%, 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 -9.5 | GERP -2.5 |
| Overall | ||
| CADD | 0.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.273%
African / African-American · 146/53,398 alleles
Filtering AF
0.237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.223%
Overall
0.0386%
447/1,156,846 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.273% | 366 |
| Admixed American | 0.0744% | 1,344 |
| Remaining individualsnot grpmax-eligible | 0.0396% | 2,523 |
| South Asian | 0.0388% | 2,579 |
| European (non-Finnish) | 0.0272% | 3,682 |
| Middle Eastern | 0.0242% | 4,130 |
| East Asian | 0.00332% | 30,123 |
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.Pro253=
- Coding
- c.759G>A
- MANE Select
- NM_031462
- dbSNP
- rs138311396
- Type
- single nucleotide variant
- Location
- chrX:150769064 (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-pro253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown