CHRND p.Asp398=
c.1194C>T · VCV3614101
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
Conditions
1
lethal multiple pterygium syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.3, phastCons 1 |
| Overall | ||
| CADD | 11.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,180,046 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.00041%
6/1,461,776 alleles · very rare
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
- CHRND
- Protein
- p.Asp398=
- Coding
- c.1194C>T
- MANE Select
- NM_000751
- Type
- single nucleotide variant
- Location
- chr2:232534077 (GRCh38)
- Gene constraint
- LOEUF 0.848 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.21 · 25 PDB
- Residue 398
- a UniProt-annotated variant site (in a breast cancer sample; somatic mutation)
Similar variants
- CHRND c.1252+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHRND c.821-2A>C Pathogenic/Likely pathogenic ★★ same condition
- CHRND c.933-2A>G Likely pathogenic ★★ same condition
- CHRND p.Arg336Gln Likely pathogenic ★★ same condition
- CHRND p.Arg43Trp Pathogenic/Likely pathogenic ★★ same condition
- CHRND p.Cys257Arg Pathogenic/Likely pathogenic ★★ same condition
- CHRND p.Trp78Ter Pathogenic ★★ same condition
- CHRND p.Trp83Ter Pathogenic/Likely pathogenic ★★ same condition
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/chrnd-p-asp398 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown