Is USB1 p.Arg130His (c.389G>A) pathogenic?

USB1 p.Arg130His (c.389G>A) is classified Uncertain significance in USB1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-30). AlphaMissense: likely benign (0.1561); Ultra-rare (popmax 0.0164%, mid); Associated with Inborn genetic diseases.

What condition is associated with USB1 p.Arg130His (c.389G>A)?

USB1 p.Arg130His (c.389G>A) is associated with Inborn genetic diseases (ClinVar).

How common is USB1 p.Arg130His (c.389G>A) in the general population?

USB1 p.Arg130His (c.389G>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about USB1 p.Arg130His (c.389G>A)?

AlphaMissense predicts likely benign (score 0.1561) — an in-silico prediction, not a clinical call.

USB1 p.Arg130His

c.389G>A · VCV3466484

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1561 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1561	likely benign
REVEL	0.42	indeterminate
SaProt	LLR -11.42	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.8, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 19 kb · p 0.36 · regional, not allelic
Overall
CADD	27.1	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

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.00062% 10/1,613,952 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
African / African-American	0.00668%	14,970
Remaining individualsnot grpmax-eligible	0.0016%	62,488
South Asian	0.0011%	91,076
European (non-Finnish)	0.000169%	590,019

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: USB1
Protein: p.Arg130His
Coding: c.389G>A
MANE Select: NM_024598
Type: single nucleotide variant
Location: chr16:58010052 (GRCh38)
Gene constraint: LOEUF 1.016 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.91 · 5 PDB
Residue 130: a β-strand

Full USB1 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

USB1 p.Arg130Cys Uncertain significance ★★ ⚠ same residue
USB1 p.Arg130= Likely benign ★ same residue
USB1 p.Arg130Pro Uncertain significance ★ ⚠ same residue
USB1 p.Ala106Ser Uncertain significance ★★ ⚠ same condition
USB1 p.Ala218Thr Uncertain significance ★★ ⚠ same condition
USB1 p.Ala218Val Uncertain significance ★★ ⚠ same condition
USB1 p.Arg112Gln Uncertain significance ★★ ⚠ same condition
USB1 p.Arg112Trp 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/usb1-p-arg130his (accessed [today's date]).

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