Is FTCD p.Val99Ile (c.295G>A) pathogenic?

FTCD p.Val99Ile (c.295G>A) is classified Uncertain significance in FTCD (ClinVar, Single submitter, 1 submitter; last evaluated 2021-02-24). AlphaMissense: likely benign (0.0908); Ultra-rare (popmax 0.0334%, mid); Associated with Inborn genetic diseases.

What condition is associated with FTCD p.Val99Ile (c.295G>A)?

FTCD p.Val99Ile (c.295G>A) is associated with Inborn genetic diseases (ClinVar).

How common is FTCD p.Val99Ile (c.295G>A) in the general population?

FTCD p.Val99Ile (c.295G>A) is ultra-rare (popmax 0.0334%, mid) (gnomAD).

What do computational predictors say about FTCD p.Val99Ile (c.295G>A)?

AlphaMissense predicts likely benign (score 0.0908) — an in-silico prediction, not a clinical call.

FTCD p.Val99Ile

c.295G>A · rs376899030 · VCV2229419

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0908 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0334%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0908	likely benign
REVEL	0.287	benign-leaning
SaProt	LLR -6.28	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP 0.23, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 19 kb · p 0.00063 · regional, not allelic
Overall
CADD	21.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0334% Middle Eastern · 2/5,990 alleles

Filtering AF 0.0104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00827%

Overall 0.00142% 22/1,553,812 alleles · ultra-rare exomes 13/1,401,576 · genomes 9/152,236 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0334%	2,995
African / African-American	0.0177%	5,651
Remaining individualsnot grpmax-eligible	0.00332%	30,119
Admixed American	0.00195%	51,312
South Asian	0.00118%	84,436
European (non-Finnish)	0.000261%	382,898

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.Val99Ile
Coding: c.295G>A
MANE Select: NM_206965
dbSNP: rs376899030
Type: single nucleotide variant
Location: chr21:46152979 (GRCh38)
Gene constraint: LOEUF 1.61 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 95.30
Residue 99: the 'formiminotransferase n-subdomain' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FTCD p.Val99Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
FTCD p.Arg255Ter Pathogenic ★★ same condition
FTCD p.Val99fs Pathogenic/Likely pathogenic ★★ same residue
FTCD p.Ala108Thr Uncertain significance ★★ ⚠ same condition
FTCD p.Ala159Val Uncertain significance ★★ ⚠ same condition
FTCD p.Ala352Val Uncertain significance ★★ ⚠ same condition
FTCD p.Ala361Val Uncertain significance ★★ same condition
FTCD p.Ala418Thr 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-val99ile (accessed [today's date]).

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