Is FERMT3 p.Gln396= (c.1188G>A) pathogenic?

FERMT3 p.Gln396= (c.1188G>A) is classified Conflicting classifications of pathogenicity in FERMT3 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-19). Rare (popmax 0.131%, nfe); Associated with leukocyte adhesion deficiency 3.

What condition is associated with FERMT3 p.Gln396= (c.1188G>A)?

FERMT3 p.Gln396= (c.1188G>A) is associated with leukocyte adhesion deficiency 3 (ClinVar).

How common is FERMT3 p.Gln396= (c.1188G>A) in the general population?

FERMT3 p.Gln396= (c.1188G>A) is rare (popmax 0.131%, nfe) (gnomAD).

How is Leukocyte adhesion deficiency inherited?

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

FERMT3 p.Gln396=

c.1188G>A · rs148021416 · VCV193746

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.131%, nfe)

Conditions

leukocyte adhesion deficiency 3

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 3.9	GERP -2.7, phastCons 1
Overall
CADD	5.195	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.131% European (non-Finnish) · 1,548/1,179,972 alleles

Filtering AF 0.126% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.124%

Overall 0.104% 1,680/1,613,632 alleles · rare exomes 1,554/1,461,410 · genomes 126/152,222 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.131%	762
Remaining individualsnot grpmax-eligible	0.0896%	1,116
Admixed American	0.0883%	1,132
African / African-American	0.0213%	4,689
Ashkenazi Jewishnot grpmax-eligible	0.0135%	7,400
Finnishnot grpmax-eligible	0.00314%	31,804
South Asian	0.0011%	91,082

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: FERMT3
Protein: p.Gln396=
Coding: c.1188G>A
MANE Select: NM_031471
dbSNP: rs148021416
Type: single nucleotide variant
Location: chr11:64219999 (GRCh38)
Gene constraint: LOEUF 0.556 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 83.80 · 6 PDB
Residue 396: the ferm domain; the ph domain

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 p.Gln396Arg Uncertain significance ★ ⚠ same residue
FERMT3 p.Arg573Ter Pathogenic/Likely pathogenic ★★ same condition
FERMT3 p.Ala109Thr Uncertain significance ★★ ⚠ same condition
FERMT3 p.Ala338Val Uncertain significance ★★ ⚠ same condition
FERMT3 p.Ala570Thr Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg103Gln Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg111His Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg129His 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-gln396 (accessed [today's date]).

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