Is FERMT3 p.Met181fs (c.540del) pathogenic?

FERMT3 p.Met181fs (c.540del) is classified Pathogenic in FERMT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-17). No gnomAD frequency available for this variant; Associated with leukocyte adhesion deficiency 3.

What condition is associated with FERMT3 p.Met181fs (c.540del)?

FERMT3 p.Met181fs (c.540del) is associated with leukocyte adhesion deficiency 3 (ClinVar).

How common is FERMT3 p.Met181fs (c.540del) in the general population?

FERMT3 p.Met181fs (c.540del) is no gnomAD frequency available for this variant (gnomAD).

How is Leukocyte adhesion deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

FERMT3 p.Met181fs

c.540del · rs2134845306 · VCV1453537

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

leukocyte adhesion deficiency 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.7	GERP -1.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FERMT3
Protein: p.Met181fs
Coding: c.540del
MANE Select: NM_031471
dbSNP: rs2134845306
Type: Deletion
Location: chr11:64211296 (GRCh38)
Gene constraint: LOEUF 0.556 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 83.80 · 6 PDB

Full FERMT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

leukocyte adhesion deficiency 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Leukocyte adhesion deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

FERMT3 c.1671-4_1671del Likely pathogenic ★ same condition
FERMT3 c.787-14_788del Likely pathogenic ★ same condition
FERMT3 p.Asp393fs Pathogenic ★ same condition
FERMT3 p.Gln75fs Pathogenic ★ same condition
FERMT3 p.Glu283fs Pathogenic ★ same condition
FERMT3 p.His488fs Pathogenic ★ same condition
FERMT3 p.Lys222fs Pathogenic ★ same condition
FERMT3 c.1311+13_1311+29del 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/fermt3-p-met181fs (accessed [today's date]).

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