Is DCPS p.Glu29Asp (c.87G>T) pathogenic?

DCPS p.Glu29Asp (c.87G>T) is classified Conflicting classifications of pathogenicity in DCPS (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-06-01). AlphaMissense: likely benign (0.0811); Low-frequency (popmax 1.44%, mid); Associated with Inborn genetic diseases.

What condition is associated with DCPS p.Glu29Asp (c.87G>T)?

DCPS p.Glu29Asp (c.87G>T) is associated with Inborn genetic diseases, Al-Raqad syndrome (ClinVar).

How common is DCPS p.Glu29Asp (c.87G>T) in the general population?

DCPS p.Glu29Asp (c.87G>T) is low-frequency (popmax 1.44%, mid) (gnomAD).

What do computational predictors say about DCPS p.Glu29Asp (c.87G>T)?

AlphaMissense predicts likely benign (score 0.0811) — an in-silico prediction, not a clinical call.

DCPS p.Glu29Asp

c.87G>T · rs147935593 · VCV500319

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0811 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.44%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0811	likely benign
REVEL	0.024	moderately benign-leaning
SaProt	LLR -7.27	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 0.46	GERP -4.5
Regional constraint	o/e 1.06	unconstrained · MANE · 42 kb · p 0.2 · regional, not allelic
Overall
CADD	4.278	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.44% Middle Eastern · 87/6,062 alleles

Filtering AF 1.19% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1%

Overall 0.0508% 820/1,614,276 alleles · low-frequency

Ancestry group	Frequency	1 in
Middle Easterngrpmax	1.44%	70
Ashkenazi Jewishnot grpmax-eligible	0.388%	257
Admixed American	0.123%	811
Remaining individualsnot grpmax-eligible	0.117%	856
European (non-Finnish)	0.0363%	2,757
African / African-American	0.0266%	3,754
South Asian	0.0231%	4,338
Finnishnot grpmax-eligible	0.00312%	32,021

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.Glu29Asp
Coding: c.87G>T
MANE Select: NM_014026
dbSNP: rs147935593
Type: single nucleotide variant
Location: chr11:126304167 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 29: 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

Also linked: Al-Raqad syndrome

Similar variants

DCPS p.Arg152Ter Likely pathogenic ★★ same condition
DCPS p.Ala184Thr Uncertain significance ★★ ⚠ same condition
DCPS p.Arg145Cys Uncertain significance ★★ ⚠ same condition
DCPS p.Pro235Leu Uncertain significance ★★ ⚠ same condition
DCPS p.Gln105= Benign ★★ same condition
DCPS p.Phe63= Benign ★★ same condition
DCPS c.201+1G>T Likely pathogenic ★ same condition
DCPS p.Glu286Ter 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/dcps-p-glu29asp (accessed [today's date]).

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