Is ODC1 p.Ala413Val (c.1238C>T) pathogenic?

ODC1 p.Ala413Val (c.1238C>T) is classified Uncertain significance in ODC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-20). AlphaMissense: likely benign (0.1057); Ultra-rare (popmax 0.0165%, mid); Associated with Inborn genetic diseases.

What condition is associated with ODC1 p.Ala413Val (c.1238C>T)?

ODC1 p.Ala413Val (c.1238C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ODC1 p.Ala413Val (c.1238C>T) in the general population?

ODC1 p.Ala413Val (c.1238C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about ODC1 p.Ala413Val (c.1238C>T)?

AlphaMissense predicts likely benign (score 0.1057) — an in-silico prediction, not a clinical call.

ODC1 p.Ala413Val

c.1238C>T · rs368504231 · VCV3204031

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1057 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1057	likely benign
REVEL	0.135	moderately benign-leaning
SaProt	LLR -6.24	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 2.2	GERP -3.9, phastCons 0.013
Regional constraint	o/e 0.85	unconstrained · MANE · 3,850 bp · p 0.00073 · regional, not allelic
Overall
CADD	15.54	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 0.0165% Middle Eastern · 1/6,060 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.00229% 37/1,613,362 alleles · ultra-rare exomes 28/1,461,074 · genomes 9/152,288 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,060
East Asian	0.00892%	11,217
Admixed American	0.00668%	14,971
African / African-American	0.00666%	15,005
European (non-Finnish)	0.00178%	56,174
Remaining individualsnot grpmax-eligible	0.0016%	62,468
South Asian	0.0011%	90,942

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: ODC1
Protein: p.Ala413Val
Coding: c.1238C>T
MANE Select: NM_002539
dbSNP: rs368504231
Type: single nucleotide variant
Location: chr2:10441512 (GRCh38)
Gene constraint: LOEUF 0.617 · pLI 0.23 (gnomAD)
Structure: AlphaFold pLDDT 88.30 · 11 PDB
Residue 413: an α-helix

Full ODC1 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

ODC1 p.Ile251Met Uncertain significance ★★ ⚠ same condition
ODC1 p.Pro264Leu Uncertain significance ★★ ⚠ same condition
ODC1 p.Ala258Val Likely benign ★★ same condition
ODC1 p.Gly253Arg Benign/Likely benign ★★ same condition
ODC1 c.1241+2T>G Uncertain significance ★ same condition
ODC1 p.Ala283Ser Uncertain significance ★ ⚠ same condition
ODC1 p.Arg165Cys Uncertain significance ★ ⚠ same condition
ODC1 p.Asp204Asn 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/odc1-p-ala413val (accessed [today's date]).

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