CD44 p.Thr561=
c.1683C>T · rs149768341 · VCV782773
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.776%, mid)
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 -0.18 | GERP -5.2 |
| Overall | ||
| CADD | 0.403 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.776%
Middle Eastern · 47/6,058 alleles
Filtering AF
0.599%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.537%
Overall
0.149%
2,397/1,613,876 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.776% | 129 |
| Remaining individualsnot grpmax-eligible | 0.197% | 508 |
| Ashkenazi Jewishnot grpmax-eligible | 0.182% | 548 |
| European (non-Finnish) | 0.16% | 624 |
| Admixed American | 0.152% | 660 |
| South Asian | 0.146% | 685 |
| African / African-American | 0.0453% | 2,207 |
| Finnishnot grpmax-eligible | 0.0344% | 2,910 |
| East Asian | 0.00446% | 22,435 |
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.Thr561=
- Coding
- c.1683C>T
- MANE Select
- NM_000610
- dbSNP
- rs149768341
- Type
- single nucleotide variant
- Location
- chr11:35211322 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.31 · 7 PDB
- Residue 561
- the 'stem' 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.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-thr561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown