Is DCPS p.Pro326Arg (c.977C>G) pathogenic?

DCPS p.Pro326Arg (c.977C>G) is classified Likely benign in DCPS (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-27). AlphaMissense: likely benign (0.1082); Rare (popmax 0.442%, afr).

How common is DCPS p.Pro326Arg (c.977C>G) in the general population?

DCPS p.Pro326Arg (c.977C>G) is rare (popmax 0.442%, afr) (gnomAD).

What do computational predictors say about DCPS p.Pro326Arg (c.977C>G)?

AlphaMissense predicts likely benign (score 0.1082) — an in-silico prediction, not a clinical call.

DCPS p.Pro326Arg

c.977C>G · rs150917728 · VCV718596

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1082 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.442%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1082	likely benign
REVEL	0.162	moderately benign-leaning
SaProt	LLR -9.73	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 5.9	GERP 6.1, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 42 kb · p 0.2 · regional, not allelic
Overall
CADD	22.1	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 0.442% African / African-American · 332/75,054 alleles

Filtering AF 0.403% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.388%

Overall 0.0271% 437/1,613,688 alleles · rare exomes 247/1,461,342 · genomes 190/152,346 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.442%	226
Remaining individualsnot grpmax-eligible	0.0416%	2,404
Admixed American	0.0333%	3,001
Middle Eastern	0.033%	3,031
European (non-Finnish)	0.00475%	21,072
South Asian	0.0011%	91,084

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.Pro326Arg
Coding: c.977C>G
MANE Select: NM_014026
dbSNP: rs150917728
Type: single nucleotide variant
Location: chr11:126345576 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.18 · 11 PDB
Residue 326: an α-helix

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

Similar variants

DCPS p.Arg152Ter Likely pathogenic ★★ same type
DCPS p.Ala184Thr Uncertain significance ★★ ⚠ same type
DCPS p.Arg145Cys Uncertain significance ★★ ⚠ same type
DCPS p.Arg242Gly Uncertain significance ★★ ⚠ same type
DCPS p.Pro235Leu Uncertain significance ★★ ⚠ same type
DCPS p.Ala186= Benign/Likely benign ★★ same type
DCPS p.Ala80= Likely benign ★★ same type
DCPS p.Asp324= Likely benign ★★ same type

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-pro326arg (accessed [today's date]).

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