Is QPCTL p.Trp55Arg (c.163T>C) pathogenic?

QPCTL p.Trp55Arg (c.163T>C) is classified Uncertain significance in QPCTL (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-06). AlphaMissense: likely benign (0.2651); Absent from gnomAD v4.1.

How common is QPCTL p.Trp55Arg (c.163T>C) in the general population?

QPCTL p.Trp55Arg (c.163T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about QPCTL p.Trp55Arg (c.163T>C)?

AlphaMissense predicts likely benign (score 0.2651) — an in-silico prediction, not a clinical call.

QPCTL p.Trp55Arg

c.163T>C · rs2513642598 · VCV2281415

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2651 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,553,220)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2651	likely benign
REVEL	0.188	benign-leaning
SaProt	LLR -8.59	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 5.4	GERP 2, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 10 kb · p 0.13 · regional, not allelic
Overall
CADD	25.0	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

No allele count reported in gnomAD v4.1 (AN 1,553,220). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: QPCTL
Protein: p.Trp55Arg
Coding: c.163T>C
MANE Select: NM_017659
dbSNP: rs2513642598
Type: single nucleotide variant
Location: chr19:45692866 (GRCh38)
Gene constraint: LOEUF 1.284 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.12 · 7 PDB

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

Similar variants

QPCTL p.Arg161His Benign ★★ same type
QPCTL p.Ala159Asp Uncertain significance ★ ⚠ same type
QPCTL p.Ala212Glu Uncertain significance ★ ⚠ same type
QPCTL p.Ala213Gly Uncertain significance ★ ⚠ same type
QPCTL p.Ala273Val Uncertain significance ★ ⚠ same type
QPCTL p.Ala354Val Uncertain significance ★ ⚠ same type
QPCTL p.Ala377Asp Uncertain significance ★ ⚠ same type
QPCTL p.Arg10Cys 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/qpctl-p-trp55arg (accessed [today's date]).

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