Is CTSV p.Arg107Ser (c.319C>A) pathogenic?

CTSV p.Arg107Ser (c.319C>A) is classified Uncertain significance in CTSV (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-25). AlphaMissense: likely benign (0.2581); Absent from gnomAD v4.1.

How common is CTSV p.Arg107Ser (c.319C>A) in the general population?

CTSV p.Arg107Ser (c.319C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTSV p.Arg107Ser (c.319C>A)?

AlphaMissense predicts likely benign (score 0.2581) — an in-silico prediction, not a clinical call.

CTSV p.Arg107Ser

c.319C>A · VCV3270239

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2581 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2581	likely benign
REVEL	0.007	strongly benign-leaning
SaProt	LLR -7.58	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -1.9, phastCons 0.94
Regional constraint	o/e 0.99	unconstrained · MANE · 5,091 bp · p 0.8 · regional, not allelic
Overall
CADD	13.55	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: CTSV
Protein: p.Arg107Ser
Coding: c.319C>A
MANE Select: NM_001333
Type: single nucleotide variant
Location: chr9:97037329 (GRCh38)
Gene constraint: LOEUF 1.374 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.13 · 25 PDB

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

Similar variants

CTSV p.Arg107His Uncertain significance ★ ⚠ same residue
CTSV p.Asn179= Benign ★★ same type
CTSV p.Ala15Asp Uncertain significance ★ ⚠ same type
CTSV p.Ala186Asp Uncertain significance ★ ⚠ same type
CTSV p.Ala186Thr Uncertain significance ★ ⚠ same type
CTSV p.Ala241Ser Uncertain significance ★ ⚠ same type
CTSV p.Ala241Thr Uncertain significance ★ ⚠ same type
CTSV p.Ala79Val Uncertain significance ★ ⚠ 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/ctsv-p-arg107ser (accessed [today's date]).

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