Is FDFT1 p.Asp159= (c.477T>C) pathogenic?

FDFT1 p.Asp159= (c.477T>C) is classified Likely benign in FDFT1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-19). Very rare (popmax 0.00439%, sas); Associated with FDFT1-related disorder.

What condition is associated with FDFT1 p.Asp159= (c.477T>C)?

FDFT1 p.Asp159= (c.477T>C) is associated with FDFT1-related disorder (ClinVar).

How common is FDFT1 p.Asp159= (c.477T>C) in the general population?

FDFT1 p.Asp159= (c.477T>C) is very rare (popmax 0.00439%, sas) (gnomAD).

FDFT1 p.Asp159=

c.477T>C · VCV3351717

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00439%, sas)

Conditions

FDFT1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -3.2	GERP -2.5
Overall
CADD	3.269	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00439% South Asian · 4/91,070 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.00062% 10/1,613,370 alleles · very rare exomes 9/1,461,150 · genomes 1/152,220 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00439%	22,767
European (non-Finnish)	0.000509%	196,581

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: FDFT1
Protein: p.Asp159=
Coding: c.477T>C
MANE Select: NM_004462
Type: single nucleotide variant
Location: chr8:11821845 (GRCh38)
Gene constraint: LOEUF 1.764 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.14 · 32 PDB
Residue 159: an α-helix

Full FDFT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

FDFT1-related disorder

Similar variants

FDFT1 c.100-85G>C Uncertain significance ★★ same condition
FDFT1 c.100-145C>G Benign same condition
FDFT1 c.100-498C>T Benign same condition
FDFT1 c.198-7T>A Likely benign same condition
FDFT1 c.-2G>A Likely benign same condition
FDFT1 p.Asn67= Benign same condition
FDFT1 p.Gln369Arg Likely benign same condition
FDFT1 p.His161= Likely benign 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/fdft1-p-asp159 (accessed [today's date]).

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