CD44 p.Thr393Met
c.1178C>T · rs11607491 · VCV778041
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0898 | likely benign |
|---|---|---|
| REVEL | 0.062 | moderately benign-leaning |
| SaProt | LLR -9.01 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor loss, 24 bp away · masked 0 · deltas |
| Pangolin | Δ0.20 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -2.2 |
| Regional constraint | o/e 1.07 | unconstrained · MANE · 32 kb · p 0.099 · regional, not allelic |
| Overall | ||
| CADD | 5.949 | PHRED · no single calibrated threshold — expert panels disagree |
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 | 1.48% | 68 |
| Amishnot grpmax-eligible | 1.43% | 70 |
| Middle Easterngrpmax | 1.09% | 92 |
| Admixed American | 1.02% | 98 |
| European (non-Finnish) | 0.861% | 116 |
| Remaining individualsnot grpmax-eligible | 0.804% | 124 |
| Finnishnot grpmax-eligible | 0.708% | 141 |
| South Asian | 0.402% | 249 |
| African / African-American | 0.164% | 610 |
| East Asian | 0.00446% | 22,427 |
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
- CD44
- Protein
- p.Thr393Met
- Coding
- c.1178C>T
- MANE Select
- NM_000610
- dbSNP
- rs11607491
- Type
- single nucleotide variant
- Location
- chr11:35204536 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.31 · 7 PDB
- Residue 393
- a UniProt-annotated variant site (in); the 'stem' region; the 'disordered' region
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.Thr415= 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-thr393met (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown