Is DCPS p.Arg152Ter (c.454C>T) pathogenic?

DCPS p.Arg152Ter (c.454C>T) is classified Likely pathogenic in DCPS (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-10). Very rare (popmax 0.004%, afr); Associated with Al-Raqad syndrome.

What condition is associated with DCPS p.Arg152Ter (c.454C>T)?

DCPS p.Arg152Ter (c.454C>T) is associated with Al-Raqad syndrome (ClinVar).

How common is DCPS p.Arg152Ter (c.454C>T) in the general population?

DCPS p.Arg152Ter (c.454C>T) is very rare (popmax 0.004%, afr) (gnomAD).

DCPS p.Arg152Ter

c.454C>T · rs904572688 · VCV1331450

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Conditions

Al-Raqad syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 6
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP 6.6, phastCons 0.95
Overall
CADD	39.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/74,912 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000867% 14/1,614,024 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	24,971
Admixed American	0.00167%	59,996
South Asian	0.0011%	91,076
European (non-Finnish)	0.000763%	131,115

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.Arg152Ter
Coding: c.454C>T
MANE Select: NM_014026
dbSNP: rs904572688
Type: single nucleotide variant
Location: chr11:126331482 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 152: a β-strand

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.Arg152Gln Uncertain significance ★ ⚠ same residue
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-arg152ter (accessed [today's date]).

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