Is DCPS p.Phe63= (c.189C>T) pathogenic?

DCPS p.Phe63= (c.189C>T) is classified Benign in DCPS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-07-30). Common (popmax 63.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with Al-Raqad syndrome.

What condition is associated with DCPS p.Phe63= (c.189C>T)?

DCPS p.Phe63= (c.189C>T) is associated with Al-Raqad syndrome (ClinVar).

DCPS p.Phe63=

Q: How common is DCPS p.Phe63= (c.189C>T) in the general population?

DCPS p.Phe63= (c.189C>T) is common (popmax 63.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.189C>T · rs695029 · VCV1229675

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 63.4%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

Al-Raqad syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP -0.44, phastCons 1
Overall
CADD	18.26	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 63.4% East Asian · 28,437/44,854 alleles

Filtering AF 62.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 62.5%

Overall 22.6% 365,169/1,613,960 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	63.4%	2
Admixed American	39.2%	3
South Asian	31.9%	3
Finnishnot grpmax-eligible	24.1%	4
Remaining individualsnot grpmax-eligible	24%	4
Ashkenazi Jewishnot grpmax-eligible	23.3%	4
Middle Eastern	21.6%	5
European (non-Finnish)	20.2%	5
Amishnot grpmax-eligible	13.8%	7
African / African-American	9.49%	11

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.Phe63=
Coding: c.189C>T
MANE Select: NM_014026
dbSNP: rs695029
Type: single nucleotide variant
Location: chr11:126304269 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 63: 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.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 c.201+1G>T Likely pathogenic ★ same condition
DCPS p.Glu286Ter Likely pathogenic ★ same condition
DCPS c.201+4C>G Uncertain significance ★ same condition
DCPS p.Arg264Leu 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-phe63 (accessed [today's date]).

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