Is MASP2 p.Ser119= (c.357C>T) pathogenic?

MASP2 p.Ser119= (c.357C>T) is classified Likely benign in MASP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-21). Rare (popmax 0.102%, amr); Associated with MASP2-related disorder.

What condition is associated with MASP2 p.Ser119= (c.357C>T)?

MASP2 p.Ser119= (c.357C>T) is associated with MASP2-related disorder (ClinVar).

How common is MASP2 p.Ser119= (c.357C>T) in the general population?

MASP2 p.Ser119= (c.357C>T) is rare (popmax 0.102%, amr) (gnomAD).

MASP2 p.Ser119=

c.357C>T · rs201175329 · VCV3052063

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.102%, amr)

Conditions

MASP2-related disorder

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 -20	GERP -3.8
Overall
CADD	0.57	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.102% Admixed American · 61/60,018 alleles

Filtering AF 0.0811% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0738%

Overall 0.00595% 96/1,613,762 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.102%	984
African / African-American	0.00932%	10,724
European (non-Finnish)	0.00229%	43,705
Remaining individualsnot grpmax-eligible	0.0016%	62,500

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.Ser119=
Coding: c.357C>T
MANE Select: NM_006610
dbSNP: rs201175329
Type: single nucleotide variant
Location: chr1:11046611 (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 119: the cub 1 domain

Full MASP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MASP2-related disorder

Similar variants

MASP2 p.Val311Ile Conflicting classifications of pathogenicity ★ ⚠ same condition
MASP2 p.Ala619= Likely benign same condition
MASP2 p.Arg563= Likely benign same condition
MASP2 p.Arg609= Likely benign same condition
MASP2 p.Gly464Ala Benign same condition
MASP2 p.Thr549= Likely benign same condition
MASP2 c.1087+8_1087+10del Uncertain significance ★ same condition
MASP2 p.Arg376Ter Likely pathogenic ★★ 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-ser119 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown