Is USP18 p.Arg262Lys (c.785G>A) pathogenic?

USP18 p.Arg262Lys (c.785G>A) is classified Uncertain significance in USP18 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-08). AlphaMissense: likely benign (0.0797); Ultra-rare (popmax 0.033%, mid); Associated with Inborn genetic diseases.

What condition is associated with USP18 p.Arg262Lys (c.785G>A)?

USP18 p.Arg262Lys (c.785G>A) is associated with Inborn genetic diseases (ClinVar).

How common is USP18 p.Arg262Lys (c.785G>A) in the general population?

USP18 p.Arg262Lys (c.785G>A) is ultra-rare (popmax 0.033%, mid) (gnomAD).

What do computational predictors say about USP18 p.Arg262Lys (c.785G>A)?

AlphaMissense predicts likely benign (score 0.0797) — an in-silico prediction, not a clinical call.

USP18 p.Arg262Lys

c.785G>A · VCV3466714

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0797 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.033%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0797	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -5.97	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.35	acceptor loss · deltas
Constraint at this position
Conservation	phyloP 0.96	phastCons 0.23
Regional constraint	o/e 0.36	constrained · MANE · 2,864 bp · p 4.3e-10 · regional, not allelic
Overall
CADD	7.665	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

Grpmax group 0.033% Middle Eastern · 2/6,056 alleles

Filtering AF 0.00582% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00242%

Overall 0.000375% 6/1,598,128 alleles · ultra-rare exomes 4/1,460,116 · genomes 2/138,012 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.033%	3,028
Admixed American	0.00343%	29,173
African / African-American	0.00147%	68,036
European (non-Finnish)	8.51e-05%	1,175,584

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: USP18
Protein: p.Arg262Lys
Coding: c.785G>A
MANE Select: NM_017414
Type: single nucleotide variant
Location: chr22:18170814 (GRCh38)
Gene constraint: LOEUF 0.459 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.60 · 2 PDB
Residue 262: the usp domain; a UniProt-annotated variant site (in ptorch2)

Full USP18 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

USP18 p.Ser2Asn Uncertain significance ★★ ⚠ same condition
USP18 p.Thr80Ile Uncertain significance ★★ ⚠ same condition
USP18 p.Arg289Gln Likely benign ★★ same condition
USP18 p.Ala212Ser Uncertain significance ★ ⚠ same condition
USP18 p.Arg114Gln Uncertain significance ★ ⚠ same condition
USP18 p.Arg119Trp Uncertain significance ★ ⚠ same condition
USP18 p.Arg171Trp Uncertain significance ★ ⚠ same condition
USP18 p.Arg238Leu 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/usp18-p-arg262lys (accessed [today's date]).

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