Is DCPS p.Gln105= (c.315G>A) pathogenic?

DCPS p.Gln105= (c.315G>A) is classified Benign in DCPS (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-07-30). Common (popmax 99.9%, eas) — too common for a highly-penetrant pathogenic allele; Associated with Al-Raqad syndrome.

What condition is associated with DCPS p.Gln105= (c.315G>A)?

DCPS p.Gln105= (c.315G>A) is associated with Al-Raqad syndrome (ClinVar).

DCPS p.Gln105=

Q: How common is DCPS p.Gln105= (c.315G>A) in the general population?

DCPS p.Gln105= (c.315G>A) is common (popmax 99.9%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.315G>A · rs637462 · VCV1255461

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 99.9%, 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 1.9	GERP -1.9, phastCons 0.97
Overall
CADD	6.196	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 99.9% East Asian · 44,806/44,830 alleles

Filtering AF 99.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 98.9%

Overall 83.5% 1,346,525/1,613,254 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	99.9%	1
African / African-American	97.2%	1
South Asian	91.6%	1
Admixed American	90.2%	1
Amishnot grpmax-eligible	86.3%	1
Ashkenazi Jewishnot grpmax-eligible	85.1%	1
Middle Eastern	84.7%	1
Remaining individualsnot grpmax-eligible	84.6%	1
European (non-Finnish)	81.1%	1
Finnishnot grpmax-eligible	79.9%	1

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.Gln105=
Coding: c.315G>A
MANE Select: NM_014026
dbSNP: rs637462
Type: single nucleotide variant
Location: chr11:126306683 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 105: 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.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
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-gln105 (accessed [today's date]).

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