Is MALT1 p.Phe813Ser (c.2438T>C) pathogenic?

MALT1 p.Phe813Ser (c.2438T>C) is classified Uncertain significance in MALT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-01). AlphaMissense: likely benign (0.1347); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with MALT1 p.Phe813Ser (c.2438T>C)?

MALT1 p.Phe813Ser (c.2438T>C) is associated with Inborn genetic diseases (ClinVar).

How common is MALT1 p.Phe813Ser (c.2438T>C) in the general population?

MALT1 p.Phe813Ser (c.2438T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MALT1 p.Phe813Ser (c.2438T>C)?

AlphaMissense predicts likely benign (score 0.1347) — an in-silico prediction, not a clinical call.

MALT1 p.Phe813Ser

c.2438T>C · VCV3542263

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1347 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1347	likely benign
REVEL	0.105	moderately benign-leaning
SaProt	LLR -4.69	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5	GERP 1.9, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 5,919 bp · p 0.0004 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Phe813Ser
Coding: c.2438T>C
MANE Select: NM_006785
Type: single nucleotide variant
Location: chr18:58747805 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI 0.64 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.09 · 27 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MALT1 p.Ala774Pro Uncertain significance ★★ ⚠ same condition
MALT1 p.Arg392His Uncertain significance ★★ ⚠ same condition
MALT1 p.Asp755Glu Uncertain significance ★★ ⚠ same condition
MALT1 p.Glu572Asp Uncertain significance ★★ ⚠ same condition
MALT1 p.His762Tyr Uncertain significance ★★ ⚠ same condition
MALT1 p.Leu586Ile Uncertain significance ★★ ⚠ same condition
MALT1 p.Lys665Glu Uncertain significance ★★ ⚠ same condition
MALT1 p.Met732Thr 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-phe813ser (accessed [today's date]).

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