CD44 p.Thr163=
c.489G>A · rs111287251 · VCV745899
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.852%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.076 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.3 | GERP -5.5 |
| Overall | ||
| CADD | 1.496 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.852%
African / African-American · 639/75,030 alleles
Filtering AF
0.797%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.775%
Overall
0.044%
711/1,614,102 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.852% | 117 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| Admixed American | 0.035% | 2,857 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.000847% | 118,001 |
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.Thr163=
- Coding
- c.489G>A
- MANE Select
- NM_000610
- dbSNP
- rs111287251
- Type
- single nucleotide variant
- Location
- chr11:35189887 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.31 · 7 PDB
- Residue 163
- the 'disordered' region
Similar variants
- CD44 p.Thr163Met Uncertain significance ★ ⚠ same residue
- 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.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-thr163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown