Is PGAP1 p.Cys623= (c.1869C>T) pathogenic?

PGAP1 p.Cys623= (c.1869C>T) is classified Likely benign in PGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-31). Absent from gnomAD v4.1; Associated with intellectual disability, autosomal recessive 42.

What condition is associated with PGAP1 p.Cys623= (c.1869C>T)?

PGAP1 p.Cys623= (c.1869C>T) is associated with intellectual disability, autosomal recessive 42 (ClinVar).

How common is PGAP1 p.Cys623= (c.1869C>T) in the general population?

PGAP1 p.Cys623= (c.1869C>T) is absent from gnomAD v4.1 (gnomAD).

PGAP1 p.Cys623=

c.1869C>T · rs2469098382 · VCV2833278

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

intellectual disability, autosomal recessive 42

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.048	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP -0.37, phastCons 1
Overall
CADD	8.313	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PGAP1
Protein: p.Cys623=
Coding: c.1869C>T
MANE Select: NM_024989
dbSNP: rs2469098382
Type: single nucleotide variant
Location: chr2:196848030 (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.Cys623Ter Pathogenic ★ same residue
PGAP1 p.Cys623fs Pathogenic ★ same residue
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

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-cys623 (accessed [today's date]).

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