MFAP1 p.Gln76=
c.228G>A · VCV4820735
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.406%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.22 | GERP -0.39, phastCons 0.97 |
| Overall | ||
| CADD | 5.412 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.406%
European (non-Finnish) · 4,789/1,180,028 alleles
Filtering AF
0.396%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.392%
Overall
0.314%
5,070/1,614,152 alleles · rare
exomes 4,737/1,461,890 · genomes 333/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.406% | 246 |
| Remaining individualsnot grpmax-eligible | 0.213% | 470 |
| Admixed American | 0.0883% | 1,132 |
| Finnishnot grpmax-eligible | 0.0671% | 1,489 |
| African / African-American | 0.0613% | 1,631 |
| East Asian | 0.00668% | 14,961 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| South Asian | 0.0022% | 45,543 |
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
- MFAP1
- Protein
- p.Gln76=
- Coding
- c.228G>A
- MANE Select
- NM_005926
- Type
- single nucleotide variant
- Location
- chr15:43817300 (GRCh38)
- Gene constraint
- LOEUF 0.412 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.84 · 14 PDB
- Residue 76
- the 'disordered' region
Similar variants
- MFAP1 p.Arg306His Uncertain significance ★ ⚠ same type
- MFAP1 p.Arg316Lys Uncertain significance ★ ⚠ same type
- MFAP1 p.Arg436Gln Uncertain significance ★ ⚠ same type
- MFAP1 p.Arg87Gln Uncertain significance ★ ⚠ same type
- MFAP1 p.Gln14His Uncertain significance ★ ⚠ same type
- MFAP1 p.Glu163Asp Uncertain significance ★ ⚠ same type
- MFAP1 p.Glu318Ala Uncertain significance ★ same type
- MFAP1 p.Glu78Asp 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/mfap1-p-gln76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown