CD44 p.Thr213=
c.639C>T · rs759698237 · VCV731701
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0274%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.013 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -5 |
| Overall | ||
| CADD | 1.805 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0274%
South Asian · 25/91,082 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.0031%
50/1,613,964 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0274% | 3,643 |
| Middle Eastern | 0.0164% | 6,084 |
| Admixed American | 0.00833% | 12,000 |
| East Asian | 0.00668% | 14,967 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| European (non-Finnish) | 0.00119% | 84,280 |
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
- CD44
- Protein
- p.Thr213=
- Coding
- c.639C>T
- MANE Select
- NM_000610
- dbSNP
- rs759698237
- Type
- single nucleotide variant
- Location
- chr11:35190037 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.31 · 7 PDB
Similar variants
- CD44 c.367+7T>C Benign ★★ same type
- CD44 p.Arg463Gln Benign ★★ same type
- CD44 p.Arg673Gln Likely benign ★★ ⚠ same type
- CD44 p.Gly462= Benign ★★ same type
- CD44 p.Ile457Val Benign ★★ same type
- CD44 p.Phe245= Benign ★★ same type
- CD44 p.Thr163= Benign ★★ same type
- CD44 p.Thr393Met 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/cd44-p-thr213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown