CHRDL1 p.Thr35=
c.105A>G · rs751250304 · VCV744646
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0668%, amr)
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 0.68 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 6.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0668%
Admixed American · 30/44,927 alleles
Filtering AF
0.0481%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0417%
Overall
0.00482%
53/1,098,927 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0668% | 1,498 |
| Remaining individualsnot grpmax-eligible | 0.0387% | 2,581 |
| African / African-American | 0.00907% | 11,021 |
| European (non-Finnish) | 0.000126% | 796,140 |
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
- CHRDL1
- Protein
- p.Thr35=
- Coding
- c.105A>G
- MANE Select
- NM_001143981
- dbSNP
- rs751250304
- Type
- single nucleotide variant
- Location
- chrX:110762797 (GRCh38)
- Structure
- AlphaFold pLDDT 69.79
- Residue 35
- the vwfc 1 domain
Similar variants
- CHRDL1 p.Glu117Ter Pathogenic/Likely pathogenic ★★ same type
- CHRDL1 p.Glu423Asp Uncertain significance ★★ ⚠ same type
- CHRDL1 p.Arg209His Benign ★★ same type
- CHRDL1 p.Gln197= Benign/Likely benign ★★ same type
- CHRDL1 p.Lys318= Benign ★★ same type
- CHRDL1 p.Met7Val Benign ★★ same type
- CHRDL1 p.Pro105= Benign/Likely benign ★★ same type
- CHRDL1 p.Thr245= Likely 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/chrdl1-p-thr35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown