MASP2 p.Ser13=
c.39G>A · rs748680631 · VCV2638216
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0369%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.41 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -2.4 |
| Overall | ||
| CADD | 5.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0369%
South Asian · 31/83,918 alleles
Filtering AF
0.0267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0233%
Overall
0.00407%
63/1,548,228 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0369% | 2,707 |
| Middle Eastern | 0.0171% | 5,848 |
| Remaining individualsnot grpmax-eligible | 0.00666% | 15,008 |
| European (non-Finnish) | 0.00227% | 44,080 |
| African / African-American | 0.00138% | 72,622 |
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.Ser13=
- Coding
- c.39G>A
- MANE Select
- NM_006610
- dbSNP
- rs748680631
- Type
- single nucleotide variant
- Location
- chr1:11047086 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.73 · 10 PDB
Similar variants
- MASP2 p.Ser13Leu Benign/Likely benign ★★ same residue
- 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
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-ser13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown