Is DCPS p.Thr316Met (c.947C>T) pathogenic?

DCPS p.Thr316Met (c.947C>T) is classified Conflicting classifications of pathogenicity in DCPS (ClinVar, Conflicting submitters, 10 submitters; last evaluated 2026-01-03). AlphaMissense: likely benign (0.1663); Rare (popmax 0.872%, sas); Associated with Al-Raqad syndrome.

What condition is associated with DCPS p.Thr316Met (c.947C>T)?

DCPS p.Thr316Met (c.947C>T) is associated with Al-Raqad syndrome (ClinVar).

How common is DCPS p.Thr316Met (c.947C>T) in the general population?

DCPS p.Thr316Met (c.947C>T) is rare (popmax 0.872%, sas) (gnomAD).

What do computational predictors say about DCPS p.Thr316Met (c.947C>T)?

AlphaMissense predicts likely benign (score 0.1663) — an in-silico prediction, not a clinical call.

DCPS p.Thr316Met

c.947C>T · rs137941190 · VCV372235

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 10 submitters

AlphaMissense

likely benign

0.1663 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.872%, sas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Al-Raqad syndrome

Computational evidence

Protein change
AlphaMissense	0.1663	likely benign
REVEL	0.765	pathogenic-leaning
SaProt	LLR -14.06	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 5.1, phastCons 0.99
Regional constraint	o/e 1.06	unconstrained · MANE · 42 kb · p 0.2 · regional, not allelic
Overall
CADD	24.2	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 0.872% South Asian · 794/91,088 alleles

Filtering AF 0.821% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.801%

Overall 0.0551% 889/1,613,974 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.872%	115
Middle Eastern	0.099%	1,010
East Asian	0.0446%	2,244
Remaining individualsnot grpmax-eligible	0.0416%	2,404
Admixed American	0.005%	20,008
European (non-Finnish)	0.00322%	31,053
Finnishnot grpmax-eligible	0.00157%	63,804
African / African-American	0.00133%	75,060

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.Thr316Met
Coding: c.947C>T
MANE Select: NM_014026
dbSNP: rs137941190
Type: single nucleotide variant
Location: chr11:126345546 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 316: a UniProt-annotated variant site (in ars; results in a severe decrease of decapase activity)

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-thr316met (accessed [today's date]).

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