Is FASN p.Ser16= (c.48G>A) pathogenic?

FASN p.Ser16= (c.48G>A) is classified Benign in FASN (ClinVar, Single submitter, 2 submitters; last evaluated 2025-12-03). Rare (popmax 0.113%, amr); Associated with Epileptic encephalopathy.

What condition is associated with FASN p.Ser16= (c.48G>A)?

FASN p.Ser16= (c.48G>A) is associated with Epileptic encephalopathy (ClinVar).

How common is FASN p.Ser16= (c.48G>A) in the general population?

FASN p.Ser16= (c.48G>A) is rare (popmax 0.113%, amr) (gnomAD).

FASN p.Ser16=

c.48G>A · rs766051789 · VCV767460

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.113%, amr)

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 -14	GERP -2.3
Overall
CADD	0.824	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.113% Admixed American · 68/60,012 alleles

Filtering AF 0.0917% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0838%

Overall 0.0102% 164/1,612,782 alleles · rare exomes 151/1,460,536 · genomes 13/152,246 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.113%	883
Ashkenazi Jewishnot grpmax-eligible	0.0372%	2,691
African / African-American	0.00667%	14,991
European (non-Finnish)	0.00653%	15,325
Remaining individualsnot grpmax-eligible	0.0032%	31,237
South Asian	0.0011%	91,088

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.Ser16=
Coding: c.48G>A
MANE Select: NM_004104
dbSNP: rs766051789
Type: single nucleotide variant
Location: chr17:82096398 (GRCh38)
Gene constraint: LOEUF 0.284 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.65 · 34 PDB
Residue 16: the ketosynthase family 3 (ks3) domain; a β-strand

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-ser16 (accessed [today's date]).

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