MASP1 p.Phe549=
c.1647C>T · rs72549170 · VCV1188798
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.99%, afr)
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 -0.45 | GERP -4.5 |
| Overall | ||
| CADD | 7.277 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.99%
African / African-American · 2,997/75,050 alleles
Filtering AF
3.87%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.83%
Overall
0.234%
3,785/1,614,216 alleles · low-frequency
exomes 2,024/1,461,874 · genomes 1,761/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.99% | 25 |
| Admixed American | 0.37% | 270 |
| Remaining individualsnot grpmax-eligible | 0.325% | 308 |
| Middle Eastern | 0.215% | 465 |
| East Asian | 0.0423% | 2,362 |
| European (non-Finnish) | 0.027% | 3,699 |
| South Asian | 0.0132% | 7,590 |
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
- MASP1
- Protein
- p.Phe549=
- Coding
- c.1647C>T
- MANE Select
- NM_139125 · reported on NM_001879
- dbSNP
- rs72549170
- Type
- single nucleotide variant
- Location
- chr3:187225418 (GRCh38)
- Gene constraint
- LOEUF 0.874 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.50 · 9 PDB
- Residue 549
- a turn; a UniProt-annotated variant site (in 3mc1); the peptidase s1 domain
Similar variants
- MASP1 p.Asn549Lys Uncertain significance ★ same residue
- MASP1 c.238-2A>T Pathogenic/Likely pathogenic ★★ same type
- MASP1 p.Lys337Ter Pathogenic/Likely pathogenic ★★ same type
- MASP1 p.Ala489Thr Uncertain significance ★★ ⚠ same type
- MASP1 p.Arg119Gln Uncertain significance ★★ ⚠ same type
- MASP1 p.Arg503His Uncertain significance ★★ same type
- MASP1 p.Arg596Met Uncertain significance ★★ ⚠ same type
- MASP1 p.Glu105Asp 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/masp1-p-phe549 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown