Is FIG4 p.Leu159= (c.477A>G) pathogenic?

FIG4 p.Leu159= (c.477A>G) is classified Likely benign in FIG4 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-19). Ultra-rare (popmax 0.018%, eas); Associated with Charcot-Marie-Tooth disease type 4.

What condition is associated with FIG4 p.Leu159= (c.477A>G)?

FIG4 p.Leu159= (c.477A>G) is associated with Charcot-Marie-Tooth disease type 4 (ClinVar).

How common is FIG4 p.Leu159= (c.477A>G) in the general population?

FIG4 p.Leu159= (c.477A>G) is ultra-rare (popmax 0.018%, eas) (gnomAD).

FIG4 p.Leu159=

c.477A>G · rs769256280 · VCV1584562

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.018%, eas)

Conditions

Charcot-Marie-Tooth disease type 4

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 -1.6	GERP -4.1
Overall
CADD	1.115	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.018% East Asian · 8/44,340 alleles

Filtering AF 0.00893% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00647%

Overall 0.000849% 13/1,531,394 alleles · ultra-rare exomes 12/1,381,404 · genomes 1/149,990 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.018%	5,542
Admixed American	0.00168%	59,542
European (non-Finnish)	0.000359%	278,664

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: FIG4
Protein: p.Leu159=
Coding: c.477A>G
MANE Select: NM_014845
dbSNP: rs769256280
Type: single nucleotide variant
Location: chr6:109732667 (GRCh38)
Gene constraint: LOEUF 0.966 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.65 · 1 PDB
Residue 159: the sac domain

Full FIG4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Charcot-Marie-Tooth disease type 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FIG4 p.Leu159Val Uncertain significance ★ same residue
FIG4 c.1040-1G>A Likely pathogenic ★★ same condition
FIG4 c.1584-1G>T Likely pathogenic ★★ same condition
FIG4 c.1948+1G>A Likely pathogenic ★★ same condition
FIG4 c.1949-10T>G Pathogenic/Likely pathogenic ★★ same condition
FIG4 c.2459+1G>A Pathogenic ★★ same condition
FIG4 c.877-2A>C Pathogenic/Likely pathogenic ★★ same condition
FIG4 p.Arg152Ter Pathogenic/Likely pathogenic ★★ 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/fig4-p-leu159 (accessed [today's date]).

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