CD44 p.Ser672=
c.2016T>C · VCV3264837
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.107%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.162 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.039 | GERP -3.5, phastCons 0.85 |
| Overall | ||
| CADD | 7.893 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.107%
African / African-American · 80/75,048 alleles
Filtering AF
0.0877%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0808%
Overall
0.0057%
92/1,613,982 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.107% | 938 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,417 |
| Admixed American | 0.005% | 20,009 |
| European (non-Finnish) | 0.000254% | 393,278 |
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.Ser672=
- Coding
- c.2016T>C
- MANE Select
- NM_000610
- Type
- single nucleotide variant
- Location
- chr11:35221724 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.31 · 7 PDB
- Residue 672
- a modified residue (phosphoserine; by pkc)
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-ser672 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown