Is GALNS p.Pro30= (c.90C>G) pathogenic?

GALNS p.Pro30= (c.90C>G) is classified Likely benign in GALNS (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-13). Very rare (popmax 8.65e-05%, nfe); Associated with mucopolysaccharidosis type 4A.

What condition is associated with GALNS p.Pro30= (c.90C>G)?

GALNS p.Pro30= (c.90C>G) is associated with mucopolysaccharidosis type 4A (ClinVar).

How common is GALNS p.Pro30= (c.90C>G) in the general population?

GALNS p.Pro30= (c.90C>G) is very rare (popmax 8.65e-05%, nfe) (gnomAD).

How is Mucopolysaccharidosis type 4 inherited?

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

GALNS p.Pro30=

c.90C>G · rs1967938638 · VCV1643967

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.65e-05%, nfe)

Conditions

mucopolysaccharidosis type 4A

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.62	GERP -1.4, phastCons 1
Overall
CADD	12.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.65e-05% European (non-Finnish) · 1/1,155,662 alleles

Overall 6.48e-05% 1/1,543,886 alleles · very rare exomes 1/1,392,934 · genomes 0/150,952 · joint denominator

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: GALNS
Protein: p.Pro30=
Coding: c.90C>G
MANE Select: NM_000512
dbSNP: rs1967938638
Type: single nucleotide variant
Location: chr16:88856788 (GRCh38)

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

Disease context

mucopolysaccharidosis type 4A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mucopolysaccharidosis type 4 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: <1 / 1 000 000 (Sweden)

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/galns-p-pro30 (accessed [today's date]).

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