CHRDL1 p.Pro105=
c.315C>A · rs138293229 · VCV2067870
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0399%, 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 0.13 | GERP -2.1, phastCons 0.29 |
| Overall | ||
| CADD | 5.167 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0399%
European (non-Finnish) · 356/891,586 alleles
Filtering AF
0.0365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0352%
Overall
0.032%
386/1,206,084 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0399% | 2,504 |
| Finnishnot grpmax-eligible | 0.0322% | 3,109 |
| Remaining individualsnot grpmax-eligible | 0.0274% | 3,652 |
| Admixed American | 0.00436% | 22,912 |
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.Pro105=
- Coding
- c.315C>A
- MANE Select
- NM_001143981
- dbSNP
- rs138293229
- Type
- single nucleotide variant
- Location
- chrX:110721517 (GRCh38)
- Structure
- AlphaFold pLDDT 69.79
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.Thr245= Likely benign ★★ same type
- CHRDL1 p.Thr35= 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-pro105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown