Is DCPS p.Asp16Ala (c.47A>C) pathogenic?

DCPS p.Asp16Ala (c.47A>C) is classified Uncertain significance in DCPS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-29). AlphaMissense: likely benign (0.0617); Ultra-rare (popmax 0.0362%, sas); Associated with Inborn genetic diseases.

What condition is associated with DCPS p.Asp16Ala (c.47A>C)?

DCPS p.Asp16Ala (c.47A>C) is associated with Inborn genetic diseases (ClinVar).

How common is DCPS p.Asp16Ala (c.47A>C) in the general population?

DCPS p.Asp16Ala (c.47A>C) is ultra-rare (popmax 0.0362%, sas) (gnomAD).

What do computational predictors say about DCPS p.Asp16Ala (c.47A>C)?

AlphaMissense predicts likely benign (score 0.0617) — an in-silico prediction, not a clinical call.

DCPS p.Asp16Ala

c.47A>C · VCV3271113

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0617 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0362%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0617	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	LLR -6.45	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 0.059	GERP -5.6
Regional constraint	o/e 1.06	unconstrained · MANE · 42 kb · p 0.2 · regional, not allelic
Overall
CADD	8.702	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 0.0362% South Asian · 33/91,054 alleles

Filtering AF 0.0265% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0231%

Overall 0.00328% 53/1,613,938 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0362%	2,759
Admixed American	0.005%	19,996
Remaining individualsnot grpmax-eligible	0.0048%	20,835
African / African-American	0.00266%	37,538
East Asian	0.00223%	44,884
European (non-Finnish)	0.000932%	107,267

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: DCPS
Protein: p.Asp16Ala
Coding: c.47A>C
MANE Select: NM_014026
Type: single nucleotide variant
Location: chr11:126304127 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 16: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCPS p.Ala184Thr Uncertain significance ★★ ⚠ same condition
DCPS p.Arg145Cys Uncertain significance ★★ ⚠ same condition
DCPS p.Pro235Leu Uncertain significance ★★ ⚠ same condition
DCPS p.Ala186Val Uncertain significance ★ ⚠ same condition
DCPS p.Ala251Val Uncertain significance ★ ⚠ same condition
DCPS p.Ala282Thr Uncertain significance ★ ⚠ same condition
DCPS p.Ala287Thr Uncertain significance ★ ⚠ same condition
DCPS p.Ala287Val Uncertain significance ★ ⚠ 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/dcps-p-asp16ala (accessed [today's date]).

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