CD81 p.Lys116=
c.348G>A · VCV4775544
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.068 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -4, phastCons 1 |
| Overall | ||
| CADD | 8.048 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,892 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000434%
7/1,611,876 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,892 |
| European (non-Finnish) | 0.000509% | 196,649 |
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
- CD81
- Protein
- p.Lys116=
- Coding
- c.348G>A
- MANE Select
- NM_004356
- Type
- single nucleotide variant
- Location
- chr11:2395040 (GRCh38)
- Gene constraint
- LOEUF 0.702 · pLI 0.36 (gnomAD)
- Structure
- AlphaFold pLDDT 87.24 · 16 PDB
- Residue 116
- a functional site (important for interaction with integrin); an α-helix
Similar variants
- CD81 c.561+5G>A Uncertain significance ★★ same type
- CD81 p.Ala120Thr Uncertain significance ★★ ⚠ same type
- CD81 p.Ala54Val Uncertain significance ★★ ⚠ same type
- CD81 p.Arg231Gln Uncertain significance ★★ ⚠ same type
- CD81 p.Asn115Ser Uncertain significance ★★ ⚠ same type
- CD81 p.Asn141Lys Uncertain significance ★★ ⚠ same type
- CD81 p.Asn141Ser Uncertain significance ★★ ⚠ same type
- CD81 p.Asn173Asp 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/cd81-p-lys116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown