Is PGAP1 p.Gln767= (c.2301A>G) pathogenic?

PGAP1 p.Gln767= (c.2301A>G) is classified Likely benign in PGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-28). No allele count reported in gnomAD v4.1 (AN 1,598,104); Associated with intellectual disability, autosomal recessive 42.

What condition is associated with PGAP1 p.Gln767= (c.2301A>G)?

PGAP1 p.Gln767= (c.2301A>G) is associated with intellectual disability, autosomal recessive 42 (ClinVar).

How common is PGAP1 p.Gln767= (c.2301A>G) in the general population?

PGAP1 p.Gln767= (c.2301A>G) is no allele count reported in gnomAD v4.1 (AN 1,598,104) (gnomAD).

PGAP1 p.Gln767=

c.2301A>G · rs1700506024 · VCV2048656

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,598,104)

Conditions

intellectual disability, autosomal recessive 42

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 1.9	GERP 1.8, phastCons 1
Overall
CADD	8.709	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,598,104). 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: PGAP1
Protein: p.Gln767=
Coding: c.2301A>G
MANE Select: NM_024989
dbSNP: rs1700506024
Type: single nucleotide variant
Location: chr2:196844560 (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.Gln466Ter Pathogenic ★★ same condition
PGAP1 p.Gln555Ter Pathogenic/Likely pathogenic ★★ same condition
PGAP1 p.Tyr758Ter Pathogenic/Likely pathogenic ★★ same condition
PGAP1 p.Ala298Thr Uncertain significance ★★ ⚠ same condition
PGAP1 p.Ala714Val Uncertain significance ★★ ⚠ same condition
PGAP1 p.Arg231Gln Uncertain significance ★★ ⚠ same condition
PGAP1 p.Arg250His Uncertain significance ★★ ⚠ same condition
PGAP1 p.Arg803Cys 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-gln767 (accessed [today's date]).

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