Is LMX1B p.Arg151= (c.453C>G) pathogenic?

LMX1B p.Arg151= (c.453C>G) is classified Likely benign in LMX1B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-09). Absent from gnomAD v4.1.

How common is LMX1B p.Arg151= (c.453C>G) in the general population?

LMX1B p.Arg151= (c.453C>G) is absent from gnomAD v4.1 (gnomAD).

LMX1B p.Arg151=

c.453C>G · VCV3652076

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.045	GERP -0.55, phastCons 0.43
Overall
CADD	10.67	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: LMX1B
Protein: p.Arg151=
Coding: c.453C>G
MANE Select: NM_001174147
Type: single nucleotide variant
Location: chr9:126690962 (GRCh38)
Gene constraint: LOEUF 0.409 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 70.79
Residue 151: the lim zinc-binding 2 domain

Full LMX1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LMX1B p.Arg151Ser Uncertain significance ★★ ⚠ same residue
LMX1B p.Arg151Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
LMX1B c.741+1G>A Pathogenic ★★ same type
LMX1B c.819+1G>A Pathogenic ★★ same type
LMX1B p.Ala236Pro Pathogenic ★★ same type
LMX1B p.Arg221Ter Pathogenic ★★ same type
LMX1B p.Arg223Gln Pathogenic ★★ same type
LMX1B p.Arg223Trp Pathogenic/Likely pathogenic ★★ 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/lmx1b-p-arg151 (accessed [today's date]).

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