Is FASN p.Pro979= (c.2937C>T) pathogenic?

FASN p.Pro979= (c.2937C>T) is classified Benign in FASN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-02). Low-frequency (popmax 2.77%, afr); Associated with Epileptic encephalopathy.

What condition is associated with FASN p.Pro979= (c.2937C>T)?

FASN p.Pro979= (c.2937C>T) is associated with Epileptic encephalopathy (ClinVar).

How common is FASN p.Pro979= (c.2937C>T) in the general population?

FASN p.Pro979= (c.2937C>T) is low-frequency (popmax 2.77%, afr) (gnomAD).

FASN p.Pro979=

c.2937C>T · rs62642479 · VCV462031

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.77%, afr)

Conditions

Epileptic encephalopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.35 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.61	GERP -2.6
Overall
CADD	0.225	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.77% African / African-American · 2,081/75,040 alleles

Filtering AF 2.67% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.63%

Overall 0.145% 2,340/1,612,630 alleles · low-frequency exomes 1,149/1,460,336 · genomes 1,191/152,294 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.77%	36
Admixed American	0.197%	509
Remaining individualsnot grpmax-eligible	0.163%	613
Middle Eastern	0.0827%	1,209
South Asian	0.00439%	22,769
European (non-Finnish)	0.00254%	39,332

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.Pro979=
Coding: c.2937C>T
MANE Select: NM_004104
dbSNP: rs62642479
Type: single nucleotide variant
Location: chr17:82087791 (GRCh38)
Gene constraint: LOEUF 0.284 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.65 · 34 PDB
Residue 979: the pks/mfas dh domain

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 p.Pro979_Thr980insAsnPro Uncertain significance ★ same residue
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

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-pro979 (accessed [today's date]).

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