Is DCD p.Ala24= (c.72C>T) pathogenic?

DCD p.Ala24= (c.72C>T) is classified Likely benign in DCD (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-25). Ultra-rare (popmax 0.0738%, amr).

How common is DCD p.Ala24= (c.72C>T) in the general population?

DCD p.Ala24= (c.72C>T) is ultra-rare (popmax 0.0738%, amr) (gnomAD).

DCD p.Ala24=

c.72C>T · rs373907849 · VCV723934

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0738%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.62	GERP -1.4
Overall
CADD	6.102	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0738% Admixed American · 39/52,862 alleles

Filtering AF 0.0554% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.049%

Overall 0.00288% 45/1,563,100 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0738%	1,355
East Asian	0.00237%	42,156
African / African-American	0.00136%	73,770
South Asian	0.00118%	84,682
European (non-Finnish)	0.00026%	384,304

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: DCD
Protein: p.Ala24=
Coding: c.72C>T
MANE Select: NM_053283
dbSNP: rs373907849
Type: single nucleotide variant
Location: chr12:54647146 (GRCh38)
Gene constraint: LOEUF 1.809 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.88 · 4 PDB
Residue 24: the 'disordered' region

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

Similar variants

DCD p.Asp71Asn Benign ★★ ⚠ same type
DCD p.Asn32Lys Uncertain significance ★ ⚠ same type
DCD p.Asn32Ser Uncertain significance ★ ⚠ same type
DCD p.Asp101Glu Uncertain significance ★ ⚠ same type
DCD p.Glu89Lys Uncertain significance ★ ⚠ same type
DCD p.Glu92Gly Uncertain significance ★ ⚠ same type
DCD p.Gly46Val Uncertain significance ★ ⚠ same type
DCD p.Gly81Arg Uncertain significance ★ ⚠ same type

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/dcd-p-ala24 (accessed [today's date]).

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