Is GNPTAB p.Pro1007fs (c.3014_3018dup) pathogenic?

GNPTAB p.Pro1007fs (c.30143018dup) is classified Pathogenic in GNPTAB (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-06). No gnomAD frequency available for this variant; Associated with mucolipidosis type III, alpha/beta.

What condition is associated with GNPTAB p.Pro1007fs (c.3014_3018dup)?

GNPTAB p.Pro1007fs (c.3014_3018dup) is associated with mucolipidosis type III, alpha/beta, mucolipidosis type II (ClinVar).

How common is GNPTAB p.Pro1007fs (c.3014_3018dup) in the general population?

GNPTAB p.Pro1007fs (c.3014_3018dup) is no gnomAD frequency available for this variant (gnomAD).

How is Mucolipidosis type III inherited?

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

GNPTAB p.Pro1007fs

c.3014_3018dup · rs2547954355 · VCV2014582

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

mucolipidosis type III, alpha/beta

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 15 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GNPTAB
Protein: p.Pro1007fs
Coding: c.3014_3018dup
MANE Select: NM_024312
dbSNP: rs2547954355
Type: Microsatellite
Location: chr12:101761243 (GRCh38)
Gene constraint: LOEUF 0.8 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.15 · 5 PDB
Residue 1007: a UniProt-annotated variant site (in mliiia); the ef-hand domain

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

Disease context

mucolipidosis type III, alpha/beta — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: mucolipidosis type II

For Mucolipidosis type III (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

GNPTAB p.Asn859fs Pathogenic ★★ same condition
GNPTAB p.Glu1187fs Pathogenic/Likely pathogenic ★★ same condition
GNPTAB p.Glu127fs Likely pathogenic ★★ same condition
GNPTAB p.Glu833fs Pathogenic/Likely pathogenic ★★ same condition
GNPTAB p.Leu1168fs Pathogenic ★★ same condition
GNPTAB p.Lys850fs Pathogenic/Likely pathogenic ★★ same condition
GNPTAB p.Met957fs Pathogenic ★★ same condition
GNPTAB p.Phe53fs 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/gnptab-p-pro1007fs (accessed [today's date]).

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