Is SAG p.Pro97del (c.286CCT[1]) pathogenic?

SAG p.Pro97del (c.286CCT[1]) is classified Uncertain significance in SAG (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-24). Very rare (popmax 0.00267%, afr).

How common is SAG p.Pro97del (c.286CCT[1]) in the general population?

SAG p.Pro97del (c.286CCT[1]) is very rare (popmax 0.00267%, afr) (gnomAD).

SAG p.Pro97del

c.286CCT[1] · rs1700355214 · VCV1046052

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

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 4.8	GERP -1.7, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,868 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000125% 2/1,606,252 alleles · very rare exomes 2/1,454,024 · genomes 0/152,228 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SAG
Protein: p.Pro97del
Coding: c.286CCT[1]
MANE Select: NM_000541
dbSNP: rs1700355214
Type: Microsatellite
Location: chr2:233320733 (GRCh38)
Structure: AlphaFold pLDDT 83.02 · 7 PDB

Full SAG gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SAG p.Lys60fs Pathogenic ★ same type
SAG c.1023-13_1023-10del Uncertain significance ★ same type
SAG c.376-3_376-2del Uncertain significance ★ same type
SAG p.Lys19del Uncertain significance ★ same type
SAG c.1046+274TG[8] Benign ★ same type
SAG c.1103-238AATAA[4] Benign ★ same type
SAG c.1113-12_1113-9del Likely benign ★ same type

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/sag-p-pro97del (accessed [today's date]).

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