Is FASN p.Pro412= (c.1236C>T) pathogenic?

FASN p.Pro412= (c.1236C>T) is classified Benign in FASN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-13). Ultra-rare (popmax 0.0833%, eas); Associated with Epileptic encephalopathy.

What condition is associated with FASN p.Pro412= (c.1236C>T)?

FASN p.Pro412= (c.1236C>T) is associated with Epileptic encephalopathy (ClinVar).

How common is FASN p.Pro412= (c.1236C>T) in the general population?

FASN p.Pro412= (c.1236C>T) is ultra-rare (popmax 0.0833%, eas) (gnomAD).

FASN p.Pro412=

c.1236C>T · rs558030339 · VCV531145

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0833%, eas)

Conditions

Epileptic encephalopathy

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 -12	GERP -3.3
Overall
CADD	1.708	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0833% East Asian · 37/44,424 alleles

Filtering AF 0.0621% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0547%

Overall 0.00848% 136/1,604,524 alleles · ultra-rare exomes 124/1,452,328 · genomes 12/152,196 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0833%	1,201
Remaining individualsnot grpmax-eligible	0.0129%	7,757
European (non-Finnish)	0.00723%	13,839
South Asian	0.00666%	15,023

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: FASN
Protein: p.Pro412=
Coding: c.1236C>T
MANE Select: NM_004104
dbSNP: rs558030339
Type: single nucleotide variant
Location: chr17:82091478 (GRCh38)
Gene constraint: LOEUF 0.284 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.65 · 34 PDB
Residue 412: an α-helix

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

Disease context

Epileptic encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FASN c.3733-3C>T Uncertain significance ★★ same condition
FASN c.655+3G>T Uncertain significance ★★ same condition
FASN p.Ala1073Ser Uncertain significance ★★ ⚠ same condition
FASN p.Ala1272Val Uncertain significance ★★ ⚠ same condition
FASN p.Ala1285Val Uncertain significance ★★ ⚠ same condition
FASN p.Ala1569Ser Uncertain significance ★★ ⚠ same condition
FASN p.Ala1684Thr Uncertain significance ★★ same condition
FASN p.Ala1686Thr 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/fasn-p-pro412 (accessed [today's date]).

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