MICOS13 p.Ser96=
c.288G>A · rs775228688 · VCV2415537
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00798%, amr)
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>A here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -2.9 |
| Overall | ||
| CADD | 0.713 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00798%
Admixed American · 4/50,112 alleles
Filtering AF
0.00266%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00155%
Overall
0.000906%
14/1,545,074 alleles · very rare
exomes 12/1,392,938 · genomes 2/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00798% | 12,528 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,860 |
| African / African-American | 0.00137% | 72,752 |
| European (non-Finnish) | 0.000699% | 143,064 |
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
- MICOS13
- Protein
- p.Ser96=
- Coding
- c.288G>A
- MANE Select
- NM_205767
- dbSNP
- rs775228688
- Type
- single nucleotide variant
- Location
- chr19:5678620 (GRCh38)
- Gene constraint
- LOEUF 1.627 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.01
Similar variants
- MICOS13 c.260-2A>G Pathogenic ★ same type
- MICOS13 c.208-3C>A Uncertain significance ★ same type
- MICOS13 p.Arg103Gly Uncertain significance ★ ⚠ same type
- MICOS13 p.Tyr105Cys Uncertain significance ★ same type
- MICOS13 c.207+13G>A Likely benign ★ same type
- MICOS13 c.207+19G>A Likely benign ★ same type
- MICOS13 c.208-20T>G Likely benign ★ same type
- MICOS13 c.259+7C>A 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/micos13-p-ser96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown