Is CTSA p.Lys429= (c.1287G>A) pathogenic?

CTSA p.Lys429= (c.1287G>A) is classified Benign/Likely benign in CTSA (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Rare (popmax 0.379%, nfe); Associated with galactosialidosis.

What condition is associated with CTSA p.Lys429= (c.1287G>A)?

CTSA p.Lys429= (c.1287G>A) is associated with galactosialidosis (ClinVar).

How common is CTSA p.Lys429= (c.1287G>A) in the general population?

CTSA p.Lys429= (c.1287G>A) is rare (popmax 0.379%, nfe) (gnomAD).

How is Galactosialidosis inherited?

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

CTSA p.Lys429=

c.1287G>A · rs41282776 · VCV771936

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

rare (popmax 0.379%, nfe)

Conditions

galactosialidosis

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 0.7	GERP -3, phastCons 1
Overall
CADD	8.121	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.379% European (non-Finnish) · 4,478/1,180,006 alleles

Filtering AF 0.37% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.366%

Overall 0.325% 5,247/1,614,126 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	2.96%	34
Finnishnot grpmax-eligible	0.406%	246
European (non-Finnish)grpmax	0.379%	264
Remaining individualsnot grpmax-eligible	0.264%	379
Admixed American	0.218%	458
Ashkenazi Jewishnot grpmax-eligible	0.172%	581
Middle Eastern	0.132%	757
South Asian	0.0955%	1,047
African / African-American	0.0533%	1,876

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CTSA
Protein: p.Lys429=
Coding: c.1287G>A
MANE Select: NM_000308
dbSNP: rs41282776
Type: single nucleotide variant
Location: chr20:45898037 (GRCh38)
Gene constraint: LOEUF 0.851 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.59 · 12 PDB
Residue 429: a β-strand

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

Disease context

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

For Galactosialidosis (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

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CTSA c.948+1G>A Likely pathogenic ★★ same condition
CTSA p.Arg375Ter Pathogenic/Likely pathogenic ★★ same condition
CTSA p.Cys256Ter Pathogenic/Likely pathogenic ★★ same condition
CTSA p.Cys281Ter Pathogenic/Likely 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/ctsa-p-lys429 (accessed [today's date]).

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