CD101 p.His883=
c.2649C>T · rs534163385 · VCV2639029
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0339%, nfe)
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 1.1 | GERP 1.6, phastCons 0.58 |
| Overall | ||
| CADD | 12.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0339%
European (non-Finnish) · 400/1,180,044 alleles
Filtering AF
0.0311%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.03%
Overall
0.0256%
414/1,614,198 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0339% | 2,950 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| African / African-American | 0.00533% | 18,762 |
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
- CD101
- Protein
- p.His883=
- Coding
- c.2649C>T
- MANE Select
- NM_001256106
- dbSNP
- rs534163385
- Type
- single nucleotide variant
- Location
- chr1:117025729 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.76
- Residue 883
- the ig-like c2-type 7 domain; a disulfide bond
Similar variants
- CD101 p.His883Asn Uncertain significance ★ ⚠ same residue
- CD101 p.His883Tyr Uncertain significance ★ ⚠ same residue
- CD101 p.Arg622His Benign ★★ same type
- CD101 p.Arg933Gln Benign ★★ ⚠ same type
- CD101 p.Asn225Ser Benign ★★ same type
- CD101 p.Leu362Pro Benign ★★ same type
- CD101 p.Ser525Arg Benign ★★ ⚠ same type
- CD101 p.Ser985= 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/cd101-p-his883 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown