Is DPCD p.Asp21Glu (c.63C>A) pathogenic?

DPCD p.Asp21Glu (c.63C>A) is classified Uncertain significance in DPCD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-27). AlphaMissense: likely benign (0.3119); Ultra-rare (popmax 0.0249%, eas).

How common is DPCD p.Asp21Glu (c.63C>A) in the general population?

DPCD p.Asp21Glu (c.63C>A) is ultra-rare (popmax 0.0249%, eas) (gnomAD).

What do computational predictors say about DPCD p.Asp21Glu (c.63C>A)?

AlphaMissense predicts likely benign (score 0.3119) — an in-silico prediction, not a clinical call.

DPCD p.Asp21Glu

c.63C>A · rs763288951 · VCV2460418

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3119 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0249%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3119	likely benign
REVEL	0.182	moderately benign-leaning
SaProt	LLR -7.45	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 0.38	GERP -2.3, phastCons 0.99
Regional constraint	o/e 1.43	unconstrained · MANE · 6,337 bp · p 0.013 · regional, not allelic
Overall
CADD	19.72	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 0.0249% East Asian · 11/44,202 alleles

Filtering AF 0.0139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0107%

Overall 0.000833% 12/1,440,226 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0249%	4,018
Remaining individualsnot grpmax-eligible	0.00162%	61,570

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: DPCD
Protein: p.Asp21Glu
Coding: c.63C>A
MANE Select: NM_015448
dbSNP: rs763288951
Type: single nucleotide variant
Location: chr10:101588399 (GRCh38)
Gene constraint: LOEUF 1.07 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.21

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

Similar variants

DPCD p.Leu156Ser Benign ★★ ⚠ same type
DPCD p.Ala155Pro Uncertain significance ★ ⚠ same type
DPCD p.Ala155Thr Uncertain significance ★ ⚠ same type
DPCD p.Ala193Thr Uncertain significance ★ ⚠ same type
DPCD p.Ala89Gly Uncertain significance ★ ⚠ same type
DPCD p.Ala89Thr Uncertain significance ★ ⚠ same type
DPCD p.Arg105Trp Uncertain significance ★ ⚠ same type
DPCD p.Arg125Cys 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/dpcd-p-asp21glu (accessed [today's date]).

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