Is CTSA p.Ser89Arg (c.265A>C) pathogenic?

CTSA p.Ser89Arg (c.265A>C) is classified Uncertain significance in CTSA (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-01). AlphaMissense: likely pathogenic (0.9977); Absent from gnomAD v4.1.

How common is CTSA p.Ser89Arg (c.265A>C) in the general population?

CTSA p.Ser89Arg (c.265A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTSA p.Ser89Arg (c.265A>C)?

AlphaMissense predicts likely pathogenic (score 0.9977) — an in-silico prediction, not a clinical call.

CTSA p.Ser89Arg

c.265A>C · rs1986980461 · VCV932379

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9977 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9977	likely pathogenic · top 1% in CTSA
REVEL	0.954	strongly pathogenic-leaning
SaProt	LLR -17.38	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 1,710 bp · p 0.19 · regional, not allelic
Overall
CADD	30.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: CTSA
Protein: p.Ser89Arg
Coding: c.265A>C
MANE Select: NM_000308
dbSNP: rs1986980461
Type: single nucleotide variant
Location: chr20:45891986 (GRCh38)
Gene constraint: LOEUF 0.851 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.59 · 12 PDB
Residue 89: a disulfide bond

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

Similar variants

CTSA p.Ser89Gly Uncertain significance ★ ⚠ same residue
CTSA c.1-2A>G Pathogenic/Likely pathogenic ★★ same type
CTSA c.358-2A>G Likely pathogenic ★★ same type
CTSA c.601-2A>G Pathogenic/Likely pathogenic ★★ same type
CTSA c.692+3A>G Pathogenic ★★ same type
CTSA c.948+1G>A Likely pathogenic ★★ same type
CTSA p.Arg375Ter Pathogenic/Likely pathogenic ★★ same type
CTSA p.Cys256Ter Pathogenic/Likely pathogenic ★★ 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/ctsa-p-ser89arg (accessed [today's date]).

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