Is PGAP1 p.Val6Thr (c.16_17inv) pathogenic?

PGAP1 p.Val6Thr (c.1617inv) is classified Uncertain significance in PGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-16). Associated with intellectual disability, autosomal recessive 42.

What condition is associated with PGAP1 p.Val6Thr (c.16_17inv)?

PGAP1 p.Val6Thr (c.16_17inv) is associated with intellectual disability, autosomal recessive 42 (ClinVar).

PGAP1 p.Val6Thr

c.16_17inv · VCV1980389

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

intellectual disability, autosomal recessive 42

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Regional constraint	o/e 0.92	unconstrained · MANE · 85 kb · p 0.0064 · regional, not allelic

Variant & gene context

Gene: PGAP1
Protein: p.Val6Thr
Coding: c.16_17inv
MANE Select: NM_024989
Type: Inversion
Location: chr2:196926600 (GRCh38)
Gene constraint: LOEUF 0.691 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 89.15

Full PGAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal recessive 42 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PGAP1 p.Arg786fs Pathogenic ★★ same condition
PGAP1 p.Gln466Ter Pathogenic ★★ same condition
PGAP1 p.Gln555Ter Pathogenic/Likely pathogenic ★★ same condition
PGAP1 p.Ile465fs Pathogenic ★★ same condition
PGAP1 p.Leu197del Pathogenic/Likely pathogenic ★★ same condition
PGAP1 p.Leu681fs Pathogenic/Likely pathogenic ★★ same condition
PGAP1 p.Tyr758Ter Pathogenic/Likely pathogenic ★★ same condition
PGAP1 p.Ala298Thr Uncertain significance ★★ ⚠ 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/pgap1-p-val6thr (accessed [today's date]).

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