MICU1 p.Arg18=
c.54A>G · rs536522504 · VCV2984917
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, eas)
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 -0.98 | GERP -4.4, phastCons 0.006 |
| Overall | ||
| CADD | 7.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
East Asian · 5/44,840 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00205%
33/1,612,626 alleles · ultra-rare
exomes 27/1,460,436 · genomes 6/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0112% | 8,968 |
| European (non-Finnish) | 0.00229% | 43,680 |
| Admixed American | 0.00167% | 59,716 |
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
- MICU1
- Protein
- p.Arg18=
- Coding
- c.54A>G
- MANE Select
- NM_001195518
- dbSNP
- rs536522504
- Type
- single nucleotide variant
- Location
- chr10:72566740 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.82 · 12 PDB
- Residue 18
- a UniProt-annotated variant site (in mpxps)
Similar variants
- MICU1 p.Arg18Ter Pathogenic ★★ same residue
- MICU1 p.Arg18Gln Uncertain significance ★★ ⚠ same residue
- MICU1 c.1072-1G>A Pathogenic ★★ same type
- MICU1 c.1072-1G>C Pathogenic ★★ same type
- MICU1 c.161+1G>A Pathogenic/Likely pathogenic ★★ same type
- MICU1 c.735+1G>A Pathogenic/Likely pathogenic ★★ same type
- MICU1 c.933+2T>C Likely pathogenic ★★ same type
- MICU1 p.Arg119Ter Pathogenic ★★ 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/micu1-p-arg18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown