Is PGAP1 p.Pro92del (c.274_276del) pathogenic?

PGAP1 p.Pro92del (c.274276del) is classified Pathogenic in PGAP1 (ClinVar, Single submitter, 2 submitters; last evaluated 2015-09-09). No gnomAD frequency available for this variant; Associated with Cerebral visual impairment and intellectual disability.

How common is PGAP1 p.Pro92del (c.274_276del) in the general population?

PGAP1 p.Pro92del (c.274_276del) is no gnomAD frequency available for this variant (gnomAD).

PGAP1 p.Pro92del

Q: What condition is associated with PGAP1 p.Pro92del (c.274_276del)?

PGAP1 p.Pro92del (c.274_276del) is associated with Cerebral visual impairment and intellectual disability, intellectual disability, autosomal recessive 42 (ClinVar).

c.274_276del · rs869025579 · VCV222979

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Cerebral visual impairment and intellectual disability

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1

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: PGAP1
Protein: p.Pro92del
Coding: c.274_276del
MANE Select: NM_024989
dbSNP: rs869025579
Type: Deletion
Location: chr2:196920022 (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

Cerebral visual impairment and intellectual disability

Also linked: intellectual disability, autosomal recessive 42

Similar variants

PGAP1 p.Pro92fs Pathogenic ★ same residue
PGAP1 p.Leu681fs Pathogenic/Likely pathogenic ★★ same condition
PGAP1 c.1426+1del Likely pathogenic ★ same condition
PGAP1 p.Asn7fs Pathogenic ★ same condition
PGAP1 p.Cys623fs Pathogenic ★ same condition
PGAP1 p.Lys308fs Pathogenic ★ same condition
PGAP1 p.Ser97fs Likely pathogenic ★ same condition
PGAP1 p.Val516fs 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/pgap1-p-pro92del (accessed [today's date]).

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