Is USB1 p.Lys117= (c.351G>A) pathogenic?

USB1 p.Lys117= (c.351G>A) is classified Likely benign in USB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-23). Absent from gnomAD v4.1.

How common is USB1 p.Lys117= (c.351G>A) in the general population?

USB1 p.Lys117= (c.351G>A) is absent from gnomAD v4.1 (gnomAD).

USB1 p.Lys117=

c.351G>A · rs1963453189 · VCV2895678

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.33	GERP -3.5, phastCons 0.95
Overall
CADD	2.12	PHRED · no single calibrated threshold — expert panels disagree

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: USB1
Protein: p.Lys117=
Coding: c.351G>A
MANE Select: NM_024598
dbSNP: rs1963453189
Type: single nucleotide variant
Location: chr16:58010014 (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 117: a β-strand

Full USB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

USB1 p.Lys117Arg Uncertain significance ★ ⚠ same residue
USB1 p.Lys117Asn Uncertain significance ★ ⚠ same residue
USB1 c.266-1G>A Pathogenic ★★ same type
USB1 p.His208Arg Likely pathogenic ★★ same type
USB1 p.Ala106Ser Uncertain significance ★★ ⚠ same type
USB1 p.Ala218Thr Uncertain significance ★★ ⚠ same type
USB1 p.Ala218Val Uncertain significance ★★ ⚠ same type
USB1 p.Arg112Gln 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/usb1-p-lys117 (accessed [today's date]).

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