Is PGAP1 p.Lys308fs (c.921_925del) pathogenic?

PGAP1 p.Lys308fs (c.921925del) 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.Lys308fs (c.921_925del) in the general population?

PGAP1 p.Lys308fs (c.921_925del) is no gnomAD frequency available for this variant (gnomAD).

PGAP1 p.Lys308fs

Q: What condition is associated with PGAP1 p.Lys308fs (c.921_925del)?

PGAP1 p.Lys308fs (c.921_925del) is associated with Cerebral visual impairment and intellectual disability, intellectual disability, autosomal recessive 42 (ClinVar).

c.921_925del · rs869025580 · VCV222980

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

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.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 1.5, 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: PGAP1
Protein: p.Lys308fs
Coding: c.921_925del
MANE Select: NM_024989
dbSNP: rs869025580
Type: Deletion
Location: chr2:196897133 (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.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.Pro92del Pathogenic ★ same condition
PGAP1 p.Pro92fs 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-lys308fs (accessed [today's date]).

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