Is FERMT3 p.Pro483= (c.1449G>A) pathogenic?

FERMT3 p.Pro483= (c.1449G>A) is classified Benign in FERMT3 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 47.1%, eas) — too common for a highly-penetrant pathogenic allele; Associated with leukocyte adhesion deficiency 3.

What condition is associated with FERMT3 p.Pro483= (c.1449G>A)?

FERMT3 p.Pro483= (c.1449G>A) is associated with leukocyte adhesion deficiency 3 (ClinVar).

How is Leukocyte adhesion deficiency inherited?

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

FERMT3 p.Pro483=

Q: How common is FERMT3 p.Pro483= (c.1449G>A) in the general population?

FERMT3 p.Pro483= (c.1449G>A) is common (popmax 47.1%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1449G>A · rs3802932 · VCV1168451

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 47.1%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

leukocyte adhesion deficiency 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.034	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -16	GERP -3.7
Overall
CADD	0.023	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 47.1% East Asian · 20,951/44,504 alleles

Filtering AF 46.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 46.3%

Overall 7.79% 125,154/1,606,958 alleles · common exomes 110,626/1,454,692 · genomes 14,528/152,266 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	47.1%	2
Admixed American	17.9%	6
African / African-American	10.4%	10
Finnishnot grpmax-eligible	9.89%	10
Remaining individualsnot grpmax-eligible	9.25%	11
Ashkenazi Jewishnot grpmax-eligible	6.71%	15
Middle Eastern	6.31%	16
European (non-Finnish)	5.87%	17
South Asian	2.66%	38
Amishnot grpmax-eligible	2.3%	43

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.Pro483=
Coding: c.1449G>A
MANE Select: NM_031471
dbSNP: rs3802932
Type: single nucleotide variant
Location: chr11:64220573 (GRCh38)
Gene constraint: LOEUF 0.556 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 83.80 · 6 PDB
Residue 483: the ferm 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.Pro483Leu Uncertain significance ★★ ⚠ same residue
FERMT3 p.Pro483Arg 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

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-pro483 (accessed [today's date]).

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