Is FTCD p.Phe51= (c.153C>T) pathogenic?

FTCD p.Phe51= (c.153C>T) is classified Likely benign in FTCD (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-29). Ultra-rare (popmax 0.029%, eas); Associated with FTCD-related disorder.

What condition is associated with FTCD p.Phe51= (c.153C>T)?

FTCD p.Phe51= (c.153C>T) is associated with FTCD-related disorder (ClinVar).

How common is FTCD p.Phe51= (c.153C>T) in the general population?

FTCD p.Phe51= (c.153C>T) is ultra-rare (popmax 0.029%, eas) (gnomAD).

FTCD p.Phe51=

c.153C>T · rs779166982 · VCV3044234

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.029%, eas)

Conditions

FTCD-related disorder

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 -9.2	GERP -2.8
Overall
CADD	2.676	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.029% East Asian · 13/44,886 alleles

Filtering AF 0.0171% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0143%

Overall 0.0145% 234/1,612,800 alleles · ultra-rare exomes 220/1,460,456 · genomes 14/152,344 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.029%	3,453
Remaining individualsnot grpmax-eligible	0.0208%	4,806
European (non-Finnish)	0.0169%	5,900
Middle Eastern	0.0165%	6,054
African / African-American	0.00533%	18,763
South Asian	0.00329%	30,360

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: FTCD
Protein: p.Phe51=
Coding: c.153C>T
MANE Select: NM_206965
dbSNP: rs779166982
Type: single nucleotide variant
Location: chr21:46154234 (GRCh38)
Gene constraint: LOEUF 1.61 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 95.30
Residue 51: the 'formiminotransferase n-subdomain' region

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

Disease context

FTCD-related disorder

Similar variants

FTCD p.Phe51Val Uncertain significance ★ ⚠ same residue
FTCD p.Arg71Ter Pathogenic/Likely pathogenic ★★ same condition
FTCD p.Arg333Ter Likely pathogenic ★ same condition
FTCD-AS1 n.71A>G Likely benign same condition
FTCD c.367+10C>G Likely benign same condition
FTCD c.*80C>G Likely benign same condition
FTCD p.Thr244= Likely benign same condition
FTCD p.Thr564Lys 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/ftcd-p-phe51 (accessed [today's date]).

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