Is FN1 p.Pro620= (c.1860G>A) pathogenic?

FN1 p.Pro620= (c.1860G>A) is classified Likely benign in FN1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-22). Ultra-rare (popmax 0.055%, amr); Associated with glomerulopathy with fibronectin deposits 2.

What condition is associated with FN1 p.Pro620= (c.1860G>A)?

FN1 p.Pro620= (c.1860G>A) is associated with glomerulopathy with fibronectin deposits 2, spondylometaphyseal dysplasia, 'corner fracture' type (ClinVar).

How common is FN1 p.Pro620= (c.1860G>A) in the general population?

FN1 p.Pro620= (c.1860G>A) is ultra-rare (popmax 0.055%, amr) (gnomAD).

How is Fibronectin glomerulopathy inherited?

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

FN1 p.Pro620=

c.1860G>A · rs147845471 · VCV720420

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.055%, amr)

Conditions

glomerulopathy with fibronectin deposits 2

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 0.35	GERP -2.3, phastCons 0.98
Overall
CADD	8.603	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.055% Admixed American · 33/59,982 alleles

Filtering AF 0.0421% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0409%

Overall 0.0369% 595/1,613,842 alleles · ultra-rare exomes 546/1,461,682 · genomes 49/152,160 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.055%	1,818
European (non-Finnish)	0.0453%	2,205
Remaining individualsnot grpmax-eligible	0.0304%	3,289
African / African-American	0.00933%	10,716
East Asian	0.00223%	44,868

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: FN1
Protein: p.Pro620=
Coding: c.1860G>A
MANE Select: NM_212482
dbSNP: rs147845471
Type: single nucleotide variant
Location: chr2:215414918 (GRCh38)
Gene constraint: LOEUF 0.404 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 70.23 · 66 PDB
Residue 620: the fibronectin type-iii 1 domain

Full FN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glomerulopathy with fibronectin deposits 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: spondylometaphyseal dysplasia, 'corner fracture' type

For Fibronectin glomerulopathy (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages

Similar variants

FN1 p.Pro620Leu Likely benign ★ same residue
FN1 p.Cys123Arg Pathogenic/Likely pathogenic ★★ same condition
FN1 p.Cys225Trp Pathogenic/Likely pathogenic ★★ same condition
FN1 p.Cys231Trp Likely pathogenic ★★ same condition
FN1 p.Cys87Trp Pathogenic ★★ same condition
FN1 p.Tyr973Cys Pathogenic ★★ same condition
FN1 c.2122+4T>C Uncertain significance ★★ same condition
FN1 c.2299+3A>T 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/fn1-p-pro620 (accessed [today's date]).

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