Is GAA p.Arg437= (c.1311C>T) pathogenic?

GAA p.Arg437= (c.1311C>T) is classified Likely benign in GAA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-07). Very rare (popmax 0.00173%, amr); Associated with Cardiovascular phenotype.

What condition is associated with GAA p.Arg437= (c.1311C>T)?

GAA p.Arg437= (c.1311C>T) is associated with Cardiovascular phenotype, glycogen storage disease II (ClinVar).

How common is GAA p.Arg437= (c.1311C>T) in the general population?

GAA p.Arg437= (c.1311C>T) is very rare (popmax 0.00173%, amr) (gnomAD).

GAA p.Arg437=

c.1311C>T · rs1234415461 · VCV1534904

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00173%, amr)

Conditions

Cardiovascular phenotype

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 Δ0.62 · evaluated, not missing
Constraint at this position
Conservation	phyloP -2.4	GERP -3.4
Overall
CADD	0.177	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00173% Admixed American · 1/57,738 alleles

Overall 6.92e-05% 1/1,445,266 alleles · very rare

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: GAA
Protein: p.Arg437=
Coding: c.1311C>T
MANE Select: NM_000152
dbSNP: rs1234415461
Type: single nucleotide variant
Location: chr17:80108813 (GRCh38)
Gene constraint: LOEUF 1.008 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.32 · 19 PDB
Residue 437: a β-strand; a UniProt-annotated variant site (in lopd); a UniProt-annotated variant site (in iopd; uncertain significance)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: glycogen storage disease II

Similar variants

GAA p.Arg437Cys Pathogenic ★★★ ⚠ same residue
GAA p.Arg437His Uncertain significance ★★ ⚠ same residue
GAA p.Arg437Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
GAA p.Arg437fs Pathogenic ★ same residue
GAA c.1076-1G>C Pathogenic ★★★ same condition
GAA c.1076-22T>G Pathogenic ★★★ same condition
GAA c.1194+5G>A Likely pathogenic ★★★ same condition
GAA c.1326+1G>A Pathogenic ★★★ 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/gaa-p-arg437 (accessed [today's date]).

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