Is AGTPBP1 p.Pro911= (c.2733T>C) pathogenic?

AGTPBP1 p.Pro911= (c.2733T>C) is classified Likely benign in AGTPBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-03). Ultra-rare (popmax 0.0558%, eas); Associated with Inborn genetic diseases.

What condition is associated with AGTPBP1 p.Pro911= (c.2733T>C)?

AGTPBP1 p.Pro911= (c.2733T>C) is associated with Inborn genetic diseases (ClinVar).

How common is AGTPBP1 p.Pro911= (c.2733T>C) in the general population?

AGTPBP1 p.Pro911= (c.2733T>C) is ultra-rare (popmax 0.0558%, eas) (gnomAD).

AGTPBP1 p.Pro911=

c.2733T>C · VCV4572895

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0558%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.21	acceptor gain, 10 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 0.21	GERP 0.75, phastCons 0.29
Overall
CADD	7.15	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0558% East Asian · 25/44,798 alleles

Filtering AF 0.0387% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0331%

Overall 0.00168% 27/1,610,972 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0558%	1,792
Remaining individualsnot grpmax-eligible	0.00321%	31,187

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: AGTPBP1
Protein: p.Pro911=
Coding: c.2733T>C
MANE Select: NM_001330701
Type: single nucleotide variant
Location: chr9:85588468 (GRCh38)
Gene constraint: LOEUF 0.556 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.95
Residue 911: the peptidase m14 domain; a UniProt-annotated variant site (in condca); a UniProt-annotated variant site (in condca; loss of tubulin deglutamylation; patient cells show lack of protein and excess of tubulin polyglutamylation)

Full AGTPBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AGTPBP1 p.Ala461Gly Uncertain significance ★★ ⚠ same condition
AGTPBP1 p.Arg1136His Uncertain significance ★★ ⚠ same condition
AGTPBP1 p.Glu1176Gly Uncertain significance ★★ ⚠ same condition
AGTPBP1 p.Ala1065Thr Uncertain significance ★ ⚠ same condition
AGTPBP1 p.Ala140Thr Uncertain significance ★ ⚠ same condition
AGTPBP1 p.Arg1008His Uncertain significance ★ ⚠ same condition
AGTPBP1 p.Arg100Gln Uncertain significance ★ ⚠ same condition
AGTPBP1 p.Arg1086Cys 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/agtpbp1-p-pro911 (accessed [today's date]).

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