ARCN1 p.Pro414=
c.1242G>A · VCV4771121
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00102%, 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 0.63 | GERP -2.6, phastCons 0.96 |
| Overall | ||
| CADD | 11.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,179,956 alleles
Filtering AF
0.000542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000428%
Overall
0.000821%
12/1,461,660 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
- ARCN1
- Protein
- p.Pro414=
- Coding
- c.1242G>A
- MANE Select
- NM_001655
- Type
- single nucleotide variant
- Location
- chr11:118597707 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.25
- Residue 414
- the mhd domain
Similar variants
- ARCN1 p.Pro414Leu Uncertain significance ★ ⚠ same residue
- ARCN1 c.654-15A>G Pathogenic/Likely pathogenic ★★ same type
- ARCN1 p.Arg170Ter Pathogenic ★★ same type
- ARCN1 p.Arg312Ter Pathogenic ★★ same type
- ARCN1 p.Arg435Ter Pathogenic/Likely pathogenic ★★ same type
- ARCN1 p.Ala169Val Uncertain significance ★★ ⚠ same type
- ARCN1 p.Arg160His Uncertain significance ★★ ⚠ same type
- ARCN1 p.Arg161His 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/arcn1-p-pro414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown