Is MALT1 p.Ser201= (c.603C>T) pathogenic?

MALT1 p.Ser201= (c.603C>T) is classified Likely benign in MALT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-21). Absent from gnomAD v4.1; Associated with combined immunodeficiency due to MALT1 deficiency.

What condition is associated with MALT1 p.Ser201= (c.603C>T)?

MALT1 p.Ser201= (c.603C>T) is associated with combined immunodeficiency due to MALT1 deficiency (ClinVar).

How common is MALT1 p.Ser201= (c.603C>T) in the general population?

MALT1 p.Ser201= (c.603C>T) is absent from gnomAD v4.1 (gnomAD).

MALT1 p.Ser201=

Q: How is Combined immunodeficiency due to MALT1 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.603C>T · VCV3651011

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

combined immunodeficiency due to MALT1 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.47 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.7	GERP 2.2, phastCons 1
Overall
CADD	12.25	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MALT1
Protein: p.Ser201=
Coding: c.603C>T
MANE Select: NM_006785
Type: single nucleotide variant
Location: chr18:58700545 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI 0.64 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.09 · 27 PDB
Residue 201: the ig-like c2-type 1 domain

Full MALT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

combined immunodeficiency due to MALT1 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Combined immunodeficiency due to MALT1 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

MALT1 p.Arg191Ter Pathogenic ★★ same condition
MALT1 c.1753+5G>A Uncertain significance ★★ same condition
MALT1 p.Ala413Val Uncertain significance ★★ ⚠ same condition
MALT1 p.Ala774Pro Uncertain significance ★★ ⚠ same condition
MALT1 p.Ala791Thr Uncertain significance ★★ ⚠ same condition
MALT1 p.Arg149Gln Uncertain significance ★★ ⚠ same condition
MALT1 p.Arg296Gln Uncertain significance ★★ ⚠ same condition
MALT1 p.Arg354Pro Uncertain significance ★★ ⚠ same condition

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/malt1-p-ser201 (accessed [today's date]).

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