Is AGBL5 p.Arg487Ter (c.1459C>T) pathogenic?

AGBL5 p.Arg487Ter (c.1459C>T) is classified Pathogenic in AGBL5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-01). Very rare (popmax 0.0011%, sas); Associated with AGBL5-related disorder.

What condition is associated with AGBL5 p.Arg487Ter (c.1459C>T)?

AGBL5 p.Arg487Ter (c.1459C>T) is associated with AGBL5-related disorder (ClinVar).

How common is AGBL5 p.Arg487Ter (c.1459C>T) in the general population?

AGBL5 p.Arg487Ter (c.1459C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

AGBL5 p.Arg487Ter

c.1459C>T · VCV3720305

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

AGBL5-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 15
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 1.5, phastCons 1
Overall
CADD	39.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,032 alleles

Filtering AF 0.000359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00026%

Overall 0.00062% 10/1,613,560 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,032
European (non-Finnish)	0.000763%	131,086

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: AGBL5
Protein: p.Arg487Ter
Coding: c.1459C>T
MANE Select: NM_021831
Type: single nucleotide variant
Location: chr2:27056716 (GRCh38)
Gene constraint: LOEUF 0.709 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.36 · 10 PDB
Residue 487: the peptidase m14 domain; a UniProt-annotated variant site (found in patients with a usher-like phenotype encompassing rp and hearing loss; likely pathogenic); a UniProt-annotated variant site (in rp75)

Full AGBL5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

AGBL5-related disorder

Similar variants

AGBL5 p.Arg487Gln Uncertain significance ★★ ⚠ same residue
AGBL5 p.Arg220Ter Pathogenic ★★ same condition
AGBL5 p.Trp592Ter Pathogenic ★★ same condition
AGBL5 p.Tyr485Ter Pathogenic/Likely pathogenic ★★ same condition
AGBL5 p.Arg313Cys Uncertain significance ★★ ⚠ same condition
AGBL5 c.2356-2A>G Likely pathogenic ★ same condition
AGBL5 p.Leu790Ter Likely pathogenic ★ same condition
AGBL5 p.Ser805Ter Likely 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/agbl5-p-arg487ter (accessed [today's date]).

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