Is QSOX1 p.Val467Glu (c.1400T>A) pathogenic?

QSOX1 p.Val467Glu (c.1400T>A) is classified Uncertain significance in QSOX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-02). AlphaMissense: ambiguous (0.4484); Absent from gnomAD v4.1.

How common is QSOX1 p.Val467Glu (c.1400T>A) in the general population?

QSOX1 p.Val467Glu (c.1400T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about QSOX1 p.Val467Glu (c.1400T>A)?

AlphaMissense predicts ambiguous (score 0.4484) — an in-silico prediction, not a clinical call.

QSOX1 p.Val467Glu

c.1400T>A · rs1572055922 · VCV3150415

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4484 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.4484	ambiguous
REVEL	0.609	indeterminate
SaProt	LLR -14.47	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 1.9, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 42 kb · p 0.17 · regional, not allelic
Overall
CADD	23.5	PHRED · no single calibrated threshold — expert panels disagree

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: QSOX1
Protein: p.Val467Glu
Coding: c.1400T>A
MANE Select: NM_002826
dbSNP: rs1572055922
Type: single nucleotide variant
Location: chr1:180194324 (GRCh38)
Gene constraint: LOEUF 0.695 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.51 · 4 PDB
Residue 467: the erv/alr sulfhydryl oxidase domain

Full QSOX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

QSOX1 p.Val467Met Uncertain significance ★ same residue
QSOX1 c.1017+6C>A Benign ★★ same type
QSOX1 p.Arg605Pro Benign ★★ same type
QSOX1 p.Arg673= Benign ★★ same type
QSOX1 p.Asn114Ser Benign ★★ same type
QSOX1 p.Pro398= Benign ★★ same type
QSOX1 p.Ala108Val Uncertain significance ★ ⚠ same type
QSOX1 p.Ala23Thr 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/qsox1-p-val467glu (accessed [today's date]).

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