Is GNPTAB p.Pro1041= (c.3123G>A) pathogenic?

GNPTAB p.Pro1041= (c.3123G>A) is classified Likely benign in GNPTAB (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-27). Rare (popmax 0.104%, afr); Associated with mucolipidosis type II.

What condition is associated with GNPTAB p.Pro1041= (c.3123G>A)?

GNPTAB p.Pro1041= (c.3123G>A) is associated with mucolipidosis type II, mucolipidosis type III, alpha/beta (ClinVar).

How common is GNPTAB p.Pro1041= (c.3123G>A) in the general population?

GNPTAB p.Pro1041= (c.3123G>A) is rare (popmax 0.104%, afr) (gnomAD).

How is Mucolipidosis type II inherited?

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

GNPTAB p.Pro1041=

c.3123G>A · rs138655417 · VCV735732

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.104%, afr)

Conditions

mucolipidosis type II

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 0.24	GERP -3.8, phastCons 0.33
Overall
CADD	3.746	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.104% African / African-American · 78/74,966 alleles

Filtering AF 0.0854% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0786%

Overall 0.00906% 146/1,611,652 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.104%	961
South Asian	0.0516%	1,937
Middle Eastern	0.0165%	6,056
Admixed American	0.00999%	10,005
Remaining individualsnot grpmax-eligible	0.00801%	12,484
European (non-Finnish)	0.000764%	130,864

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: GNPTAB
Protein: p.Pro1041=
Coding: c.3123G>A
MANE Select: NM_024312
dbSNP: rs138655417
Type: single nucleotide variant
Location: chr12:101761139 (GRCh38)
Gene constraint: LOEUF 0.8 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.15 · 5 PDB
Residue 1041: a UniProt-annotated variant site (in mliiia)

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

Disease context

mucolipidosis type II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: mucolipidosis type III, alpha/beta

For Mucolipidosis type II (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

GNPTAB c.118-1G>A Pathogenic/Likely pathogenic ★★ same condition
GNPTAB c.118-2A>G Pathogenic/Likely pathogenic ★★ same condition
GNPTAB c.1284+1G>T Pathogenic/Likely pathogenic ★★ same condition
GNPTAB c.1408+1G>T Pathogenic/Likely pathogenic ★★ same condition
GNPTAB c.1409-2A>G Pathogenic/Likely pathogenic ★★ same condition
GNPTAB c.2715+1G>A Pathogenic ★★ same condition
GNPTAB c.2715+2T>G Pathogenic ★★ same condition
GNPTAB c.324-2A>G 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/gnptab-p-pro1041 (accessed [today's date]).

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