CD48 p.Cys210Ser
c.629G>C · VCV4834924
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.5554 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
0/2 damaging
REVEL, SaProt · AlphaMissense no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.5554 | ambiguous |
|---|---|---|
| REVEL | 0.005 | strongly benign-leaning |
| SaProt | LLR -7.01 | tolerated |
| ⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.31 | GERP -0.67 |
| Regional constraint | o/e 1.07 | unconstrained · MANE · 33 kb · p 0.23 · regional, not allelic |
| Overall | ||
| CADD | 4.26 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CD48
- Protein
- p.Cys210Ser
- Coding
- c.629G>C
- MANE Select
- NM_001778
- Type
- single nucleotide variant
- Location
- chr1:160681225 (GRCh38)
- Gene constraint
- LOEUF 1.31 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.20 · 1 PDB
- Residue 210
- the ig-like c2-type 2 domain
Similar variants
- CD48 p.Thr216Ile Uncertain significance ★★ ⚠ same type
- CD48 c.652+73G>T Benign ★★ same type
- CD48 p.Gln90= Benign ★★ same type
- CD48 p.Leu30= Benign ★★ same type
- CD48 p.Thr233= Benign/Likely benign ★★ same type
- CD48 p.Ala93Thr Uncertain significance ★ ⚠ same type
- CD48 p.Arg192Met Uncertain significance ★ ⚠ same type
- CD48 p.Asn178Lys Uncertain significance ★ ⚠ 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/cd48-p-cys210ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown