Is DCD p.Asn32Ser (c.95A>G) pathogenic?

DCD p.Asn32Ser (c.95A>G) is classified Uncertain significance in DCD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-26). AlphaMissense: likely benign (0.1604); Very rare (popmax 0.000261%, nfe).

How common is DCD p.Asn32Ser (c.95A>G) in the general population?

DCD p.Asn32Ser (c.95A>G) is very rare (popmax 0.000261%, nfe) (gnomAD).

What do computational predictors say about DCD p.Asn32Ser (c.95A>G)?

AlphaMissense predicts likely benign (score 0.1604) — an in-silico prediction, not a clinical call.

DCD p.Asn32Ser

c.95A>G · VCV4237973

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1604 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000261%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1604	likely benign
REVEL	0.123	moderately benign-leaning
SaProt	LLR -4.61	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 -0.83	GERP -2.1
Regional constraint	o/e 1.04	unconstrained · MANE · 3,587 bp · p 0.63 · regional, not allelic
Overall
CADD	7.144	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 0.000261% European (non-Finnish) · 3/1,150,520 alleles

Filtering AF 6.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000213% 3/1,406,628 alleles · very rare

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.Asn32Ser
Coding: c.95A>G
MANE Select: NM_053283
Type: single nucleotide variant
Location: chr12:54647123 (GRCh38)
Gene constraint: LOEUF 1.809 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.88 · 4 PDB
Residue 32: the 'disordered' region

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

Similar variants

DCD p.Asn32Lys Uncertain significance ★ ⚠ same residue
DCD p.Asp71Asn Benign ★★ ⚠ 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
DCD p.Leu65Phe 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-asn32ser (accessed [today's date]).

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