MFAP5 p.Arg99=
c.295C>A · VCV3689140
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.48 | acceptor loss, 47 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.43 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 8.4 | GERP 0.85, phastCons 1 |
| Overall | ||
| CADD | 8.377 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,016 alleles
Overall
6.2e-05%
1/1,613,952 alleles · very rare
exomes 0/1,461,862 · genomes 1/152,090 · joint denominator
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
- MFAP5
- Protein
- p.Arg99=
- Coding
- c.295C>A
- MANE Select
- NM_003480
- Type
- single nucleotide variant
- Location
- chr12:8650542 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.79
Similar variants
- MFAP5 p.Arg99Trp Uncertain significance ★★ ⚠ same residue
- MFAP5 p.Arg99Gln Likely benign ★★ same residue
- MFAP5 c.140-3C>A Uncertain significance ★★ same type
- MFAP5 c.217+1G>T Uncertain significance ★★ same type
- MFAP5 c.247+1G>C Uncertain significance ★★ same type
- MFAP5 c.335+4A>G Uncertain significance ★★ same type
- MFAP5 c.336-3C>T Uncertain significance ★★ same type
- MFAP5 p.Arg115His 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/mfap5-p-arg99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown