CD244 p.Leu13=
c.39C>T · rs16832484 · VCV780271
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.56%, 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 1.1 | GERP 1.4, phastCons 0.85 |
| Overall | ||
| CADD | 2.514 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.56%
African / African-American · 3,420/75,012 alleles
Filtering AF
4.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.38%
Overall
0.25%
4,037/1,614,032 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.56% | 22 |
| Admixed American | 0.451% | 221 |
| Remaining individualsnot grpmax-eligible | 0.379% | 264 |
| Middle Eastern | 0.215% | 466 |
| South Asian | 0.0121% | 8,279 |
| European (non-Finnish) | 0.0072% | 13,882 |
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
- CD244
- Protein
- p.Leu13=
- Coding
- c.39C>T
- MANE Select
- NM_016382
- dbSNP
- rs16832484
- Type
- single nucleotide variant
- Location
- chr1:160862639 (GRCh38)
- Gene constraint
- LOEUF 0.501 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 71.23
Similar variants
- CD244 c.*578T>C Benign ★★ same type
- CD244 p.Ile229Val Benign ★★ same type
- CD244 c.380-3C>T Uncertain significance ★ ⚠ same type
- CD244 c.380-4C>T Uncertain significance ★ ⚠ same type
- CD244 p.Ala234Ser Uncertain significance ★ ⚠ same type
- CD244 p.Arg133Cys Uncertain significance ★ ⚠ same type
- CD244 p.Arg355His Uncertain significance ★ ⚠ same type
- CD244 p.Asn349Lys 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/cd244-p-leu13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown