Is FTCD p.Gly490= (c.1470C>T) pathogenic?

FTCD p.Gly490= (c.1470C>T) is classified Benign in FTCD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Common (popmax 40.1%, eas) — too common for a highly-penetrant pathogenic allele; Associated with formiminoglutamic aciduria.

What condition is associated with FTCD p.Gly490= (c.1470C>T)?

FTCD p.Gly490= (c.1470C>T) is associated with formiminoglutamic aciduria (ClinVar).

How is Formiminoglutamic aciduria inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

FTCD p.Gly490=

Q: How common is FTCD p.Gly490= (c.1470C>T) in the general population?

FTCD p.Gly490= (c.1470C>T) is common (popmax 40.1%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1470C>T · rs10432965 · VCV340414

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 40.1%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

formiminoglutamic aciduria

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.226	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.1	GERP -2.4
Overall
CADD	0.181	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 40.1% East Asian · 17,982/44,830 alleles

Filtering AF 39.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 39.4%

Overall 5.84% 94,254/1,613,008 alleles · common exomes 79,293/1,460,842 · genomes 14,961/152,166 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	40.1%	2
African / African-American	19.6%	5
Admixed American	9.42%	11
South Asian	8.41%	12
Middle Eastern	8.14%	12
Amishnot grpmax-eligible	7.14%	14
Remaining individualsnot grpmax-eligible	6.88%	15
Ashkenazi Jewishnot grpmax-eligible	3.95%	25
European (non-Finnish)	3.45%	29
Finnishnot grpmax-eligible	2.53%	40

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.Gly490=
Coding: c.1470C>T
MANE Select: NM_206965
dbSNP: rs10432965
Type: single nucleotide variant
Location: chr21:46137308 (GRCh38)
Gene constraint: LOEUF 1.61 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 95.30
Residue 490: the 'cyclodeaminase/cyclohydrolase' region

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

Disease context

formiminoglutamic aciduria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Formiminoglutamic aciduria (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

FTCD p.Arg255Ter Pathogenic ★★ same condition
FTCD p.Arg71Ter Pathogenic/Likely pathogenic ★★ same condition
FTCD p.Leu536Ter Pathogenic/Likely pathogenic ★★ same condition
FTCD p.Ala108Thr Uncertain significance ★★ ⚠ same condition
FTCD p.Ala159Val Uncertain significance ★★ ⚠ same condition
FTCD p.Ala368Val Uncertain significance ★★ ⚠ same condition
FTCD p.Ala418Thr Uncertain significance ★★ ⚠ same condition
FTCD p.Ala455Thr 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/ftcd-p-gly490 (accessed [today's date]).

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