Is PGAP1 p.Thr220Arg (c.659C>G) pathogenic?

PGAP1 p.Thr220Arg (c.659C>G) is classified Uncertain significance in PGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-01). AlphaMissense: likely benign (0.0645); Absent from gnomAD v4.1; Associated with hereditary spastic paraplegia.

What condition is associated with PGAP1 p.Thr220Arg (c.659C>G)?

PGAP1 p.Thr220Arg (c.659C>G) is associated with hereditary spastic paraplegia (ClinVar).

How common is PGAP1 p.Thr220Arg (c.659C>G) in the general population?

PGAP1 p.Thr220Arg (c.659C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PGAP1 p.Thr220Arg (c.659C>G)?

AlphaMissense predicts likely benign (score 0.0645) — an in-silico prediction, not a clinical call.

PGAP1 p.Thr220Arg

c.659C>G · rs774987863 · VCV1344460

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0645 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary spastic paraplegia

Computational evidence

Protein change
AlphaMissense	0.0645	likely benign
REVEL	0.169	moderately benign-leaning
SaProt	LLR -6.25	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.7	GERP 0.56, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 85 kb · p 0.0064 · regional, not allelic
Overall
CADD	17.22	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Thr220Arg
Coding: c.659C>G
MANE Select: NM_024989
dbSNP: rs774987863
Type: single nucleotide variant
Location: chr2:196902733 (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

hereditary spastic paraplegia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PGAP1 p.Thr220Met Conflicting classifications of pathogenicity ★ ⚠ same residue
PGAP1 p.Ile725Asn Uncertain significance ★★ ⚠ same condition
PGAP1 p.Lys111Glu Uncertain significance ★★ ⚠ same condition
PGAP1 p.Phe19Leu Uncertain significance ★★ ⚠ same condition
PGAP1 p.Phe451Tyr Uncertain significance ★★ ⚠ same condition
PGAP1 p.Ser798Leu Uncertain significance ★★ ⚠ same condition
PGAP1 c.1862-3C>T Benign ★★ same condition
PGAP1 p.Ala669= Benign ★★ 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-thr220arg (accessed [today's date]).

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