CHRD p.Pro880=
c.2640A>G · rs141759205 · VCV2654326
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00229%, 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 -2.7 | GERP -2.4 |
| Overall | ||
| CADD | 2.653 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00229%
European (non-Finnish) · 27/1,180,012 alleles
Filtering AF
0.00157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00134%
Overall
0.00198%
32/1,613,804 alleles · very rare
exomes 29/1,461,644 · genomes 3/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00229% | 43,704 |
| East Asian | 0.00223% | 44,894 |
| South Asian | 0.0022% | 45,547 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00133% | 74,916 |
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
- CHRD
- Protein
- p.Pro880=
- Coding
- c.2640A>G
- MANE Select
- NM_003741
- dbSNP
- rs141759205
- Type
- single nucleotide variant
- Location
- chr3:184388672 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.95 · 3 PDB
- Residue 880
- the vwfc 4 domain
Similar variants
- CHRD p.Gln608= Benign ★★ same type
- CHRD p.Gly387Ser Benign ★★ same type
- CHRD p.Pro772= Benign ★★ same type
- CHRD p.Thr301= Benign ★★ same type
- CHRD p.Thr457Ser Likely benign ★★ same type
- CHRD p.Ala251Glu Uncertain significance ★ ⚠ same type
- CHRD p.Ala251Thr Uncertain significance ★ ⚠ same type
- CHRD p.Ala27Pro 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/chrd-p-pro880 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown