MASP2 p.Pro383=
c.1149T>C · VCV4955103
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.148%, 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 -8.8 | GERP -2 |
| Overall | ||
| CADD | 0.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.148%
African / African-American · 111/75,048 alleles
Filtering AF
0.126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.117%
Overall
0.00824%
133/1,613,898 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.148% | 676 |
| Middle Eastern | 0.0165% | 6,058 |
| Admixed American | 0.015% | 6,667 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| South Asian | 0.0022% | 45,532 |
| European (non-Finnish) | 0.000509% | 196,631 |
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
- MASP2
- Protein
- p.Pro383=
- Coding
- c.1149T>C
- MANE Select
- NM_006610
- Type
- single nucleotide variant
- Location
- chr1:11030821 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.73 · 10 PDB
- Residue 383
- a disulfide bond; the sushi 2 domain
Similar variants
- MASP2 p.Arg376Ter Likely pathogenic ★★ same type
- TARDBP p.Gly294Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- MASP2 p.Ala149Val Uncertain significance ★★ ⚠ same type
- MASP2 p.Ala169Gly Uncertain significance ★★ ⚠ same type
- MASP2 p.Arg29His Uncertain significance ★★ ⚠ same type
- MASP2 p.Arg58Cys Uncertain significance ★★ ⚠ same type
- MASP2 p.Asp75Asn Uncertain significance ★★ ⚠ same type
- MASP2 p.Cys396Tyr 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/masp2-p-pro383 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown