Is DCPS p.Thr87Met (c.260C>T) pathogenic?

DCPS p.Thr87Met (c.260C>T) is classified Uncertain significance in DCPS (ClinVar, Single submitter, 2 submitters; last evaluated 2026-04-08). AlphaMissense: likely benign (0.0885); Ultra-rare (popmax 0.0165%, mid); Associated with Al-Raqad syndrome.

What condition is associated with DCPS p.Thr87Met (c.260C>T)?

DCPS p.Thr87Met (c.260C>T) is associated with Al-Raqad syndrome (ClinVar).

How common is DCPS p.Thr87Met (c.260C>T) in the general population?

DCPS p.Thr87Met (c.260C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about DCPS p.Thr87Met (c.260C>T)?

AlphaMissense predicts likely benign (score 0.0885) — an in-silico prediction, not a clinical call.

DCPS p.Thr87Met

c.260C>T · rs138737928 · VCV638276

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0885 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Al-Raqad syndrome

Computational evidence

Protein change
AlphaMissense	0.0885	likely benign
REVEL	0.193	benign-leaning
SaProt	LLR -8.56	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 4.9	GERP 1.8, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 42 kb · p 0.2 · regional, not allelic
Overall
CADD	27.0	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 0.0165% Middle Eastern · 1/6,066 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.00341% 55/1,613,708 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,066
Admixed American	0.01%	9,996
African / African-American	0.00534%	18,716
European (non-Finnish)	0.00373%	26,815

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.Thr87Met
Coding: c.260C>T
MANE Select: NM_014026
dbSNP: rs138737928
Type: single nucleotide variant
Location: chr11:126306628 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 87: an α-helix

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

Disease context

Al-Raqad syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCPS p.Arg152Ter Likely pathogenic ★★ same condition
DCPS p.Ala184Thr 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
DCPS c.201+4C>G 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-thr87met (accessed [today's date]).

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