Is DDC p.Thr69= (c.207G>A) pathogenic?

DDC p.Thr69= (c.207G>A) is classified Likely benign in DDC (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-03). Rare (popmax 0.139%, afr); Associated with aromatic L-amino acid decarboxylase deficiency.

What condition is associated with DDC p.Thr69= (c.207G>A)?

DDC p.Thr69= (c.207G>A) is associated with aromatic L-amino acid decarboxylase deficiency (ClinVar).

How common is DDC p.Thr69= (c.207G>A) in the general population?

DDC p.Thr69= (c.207G>A) is rare (popmax 0.139%, afr) (gnomAD).

How is Aromatic L-amino acid decarboxylase deficiency inherited?

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

DDC p.Thr69=

c.207G>A · rs61731774 · VCV1081221

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.139%, afr)

Conditions

aromatic L-amino acid decarboxylase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.003	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.7	GERP -5.1
Overall
CADD	6.173	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.139% African / African-American · 104/74,986 alleles

Filtering AF 0.117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.109%

Overall 0.00837% 135/1,612,200 alleles · rare exomes 76/1,459,904 · genomes 59/152,296 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.139%	721
Admixed American	0.015%	6,660
Remaining individualsnot grpmax-eligible	0.00801%	12,486
South Asian	0.00331%	30,253
European (non-Finnish)	0.00119%	84,198

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: DDC
Protein: p.Thr69=
Coding: c.207G>A
MANE Select: NM_001082971
dbSNP: rs61731774
Type: single nucleotide variant
Location: chr7:50540023 (GRCh38)
Gene constraint: LOEUF 0.922 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.88 · 8 PDB
Residue 69: the '2 x approximate tandem repeats' region

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

Disease context

aromatic L-amino acid decarboxylase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Aromatic L-amino acid decarboxylase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DDC p.Thr69Met Pathogenic/Likely pathogenic ★★ same residue
DDC c.1041+1G>A Pathogenic/Likely pathogenic ★★ same condition
DDC c.201+1G>C Likely pathogenic ★★ same condition
DDC c.201+5G>C Pathogenic/Likely pathogenic ★★ same condition
DDC c.714+4A>T Pathogenic ★★ same condition
DDC p.Ala275Thr Pathogenic/Likely pathogenic ★★ same condition
DDC p.Ala91Val Pathogenic/Likely pathogenic ★★ same condition
DDC p.Arg160Trp Pathogenic/Likely pathogenic ★★ 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/ddc-p-thr69 (accessed [today's date]).

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