Is XPR1 p.Pro338Ser (c.1012C>T) pathogenic?

XPR1 p.Pro338Ser (c.1012C>T) is classified Uncertain significance in XPR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-25). AlphaMissense: likely benign (0.1114); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with XPR1 p.Pro338Ser (c.1012C>T)?

XPR1 p.Pro338Ser (c.1012C>T) is associated with Inborn genetic diseases (ClinVar).

How common is XPR1 p.Pro338Ser (c.1012C>T) in the general population?

XPR1 p.Pro338Ser (c.1012C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about XPR1 p.Pro338Ser (c.1012C>T)?

AlphaMissense predicts likely benign (score 0.1114) — an in-silico prediction, not a clinical call.

XPR1 p.Pro338Ser

c.1012C>T · VCV3333513

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1114 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1114	likely benign
REVEL	0.097	moderately benign-leaning
SaProt	LLR -5.41	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 7.7	GERP 1.6, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 55 kb · p 5.7e-09 · regional, not allelic
Overall
CADD	19.91	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: XPR1
Protein: p.Pro338Ser
Coding: c.1012C>T
MANE Select: NM_004736
Type: single nucleotide variant
Location: chr1:180825222 (GRCh38)
Gene constraint: LOEUF 0.43 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.31 · 51 PDB
Residue 338: an α-helix

Full XPR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

XPR1 p.Ala572Val Uncertain significance ★★ ⚠ same condition
XPR1 p.Arg110Cys Uncertain significance ★★ ⚠ same condition
XPR1 p.Arg655Gly Uncertain significance ★★ ⚠ same condition
XPR1 p.Arg659Gln Uncertain significance ★★ ⚠ same condition
XPR1 p.Arg670His Uncertain significance ★★ ⚠ same condition
XPR1 p.Arg671Gln Uncertain significance ★★ ⚠ same condition
XPR1 p.Arg681Cys Uncertain significance ★★ ⚠ same condition
XPR1 p.His179Gln Uncertain significance ★★ ⚠ 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/xpr1-p-pro338ser (accessed [today's date]).

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