Is ODC1 p.Pro438fs (c.1313_1316del) pathogenic?

ODC1 p.Pro438fs (c.13131316del) is classified Likely pathogenic in ODC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-06-07). No gnomAD frequency available for this variant; Associated with neurodevelopmental disorder with alopecia and brain abnormalities.

What condition is associated with ODC1 p.Pro438fs (c.1313_1316del)?

ODC1 p.Pro438fs (c.1313_1316del) is associated with neurodevelopmental disorder with alopecia and brain abnormalities (ClinVar).

How common is ODC1 p.Pro438fs (c.1313_1316del) in the general population?

ODC1 p.Pro438fs (c.1313_1316del) is no gnomAD frequency available for this variant (gnomAD).

ODC1 p.Pro438fs

Q: How is Global developmental delay-alopecia-macrocephaly-facial dysmorphism-structural brain anomalies syndrome inherited?

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

c.1313_1316del · rs1671795191 · VCV978044

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder with alopecia and brain abnormalities

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.1	GERP -0.27, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ODC1
Protein: p.Pro438fs
Coding: c.1313_1316del
MANE Select: NM_002539
dbSNP: rs1671795191
Type: Deletion
Location: chr2:10440794 (GRCh38)
Structure: AlphaFold pLDDT 88.91

Full ODC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder with alopecia and brain abnormalities — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Global developmental delay-alopecia-macrocephaly-facial dysmorphism-structural brain anomalies syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Antenatal, Neonatal

Similar variants

ODC1 p.Asp433fs Likely pathogenic ★ same condition
ODC1 p.Pro438Ser Uncertain significance ★ ⚠ same residue
ODC1 c.1242-2A>G Pathogenic ★★ same condition
ODC1 p.Trp356fs Likely pathogenic ★ same condition
ODC1 p.Trp443Ter Likely pathogenic ★ same condition
ODC1 p.Asn256Lys Uncertain significance ★ ⚠ same condition
ODC1 p.Asp304Glu Uncertain significance ★ ⚠ same condition
ODC1 p.Asp35Asn Conflicting classifications of pathogenicity ★ ⚠ 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-pro438fs (accessed [today's date]).

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