Is FOXC2 p.Pro362Arg (c.1085C>G) pathogenic?

FOXC2 p.Pro362Arg (c.1085C>G) is classified Uncertain significance in FOXC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-20). AlphaMissense: likely benign (0.1608); Very rare (popmax 0.00147%, sas); Associated with Inborn genetic diseases.

What condition is associated with FOXC2 p.Pro362Arg (c.1085C>G)?

FOXC2 p.Pro362Arg (c.1085C>G) is associated with Inborn genetic diseases (ClinVar).

How common is FOXC2 p.Pro362Arg (c.1085C>G) in the general population?

FOXC2 p.Pro362Arg (c.1085C>G) is very rare (popmax 0.00147%, sas) (gnomAD).

What do computational predictors say about FOXC2 p.Pro362Arg (c.1085C>G)?

AlphaMissense predicts likely benign (score 0.1608) — an in-silico prediction, not a clinical call.

FOXC2 p.Pro362Arg

c.1085C>G · VCV3851214

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1608 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00147%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1608	likely benign
REVEL	0.213	benign-leaning
SaProt	LLR -5.80	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.4	GERP 1.9, phastCons 1
Regional constraint	o/e 1.27	unconstrained · MANE · 1,003 bp · p 1.1e-09 · regional, not allelic
Overall
CADD	19.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00147% South Asian · 1/67,900 alleles

Filtering AF 0.000203% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000133%

Overall 0.000565% 7/1,238,162 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00147%	67,900
European (non-Finnish)	0.000564%	177,435

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: FOXC2
Protein: p.Pro362Arg
Coding: c.1085C>G
MANE Select: NM_005251
Type: single nucleotide variant
Location: chr16:86568420 (GRCh38)
Gene constraint: LOEUF 1.807 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 56.45 · 8 PDB

Full FOXC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FOXC2 p.Pro362= Likely benign ★ same residue
FOXC2 p.Ala194Ser Uncertain significance ★★ ⚠ same condition
FOXC2 p.Ala326Gly Uncertain significance ★★ ⚠ same condition
FOXC2 p.Gly295Ser Uncertain significance ★★ ⚠ same condition
FOXC2 p.Gly314Asp Uncertain significance ★★ ⚠ same condition
FOXC2 p.Gly467Glu Uncertain significance ★★ ⚠ same condition
FOXC2 p.Ile120Val Uncertain significance ★★ ⚠ same condition
FOXC2 p.Met453Ile 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/foxc2-p-pro362arg (accessed [today's date]).

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