Is CCDC183 p.Arg237Gln (c.710G>A) pathogenic?

CCDC183 p.Arg237Gln (c.710G>A) is classified Uncertain significance in CCDC183 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-31). AlphaMissense: likely benign (0.095); Rare (popmax 0.111%, eas).

How common is CCDC183 p.Arg237Gln (c.710G>A) in the general population?

CCDC183 p.Arg237Gln (c.710G>A) is rare (popmax 0.111%, eas) (gnomAD).

What do computational predictors say about CCDC183 p.Arg237Gln (c.710G>A)?

AlphaMissense predicts likely benign (score 0.095) — an in-silico prediction, not a clinical call.

CCDC183 p.Arg237Gln

c.710G>A · rs201155882 · VCV2510711

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.095 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.111%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.095	likely benign
REVEL	0.045	moderately benign-leaning
SaProt	LLR -7.06	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 3.6	GERP 1.1, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 11 kb · p 0.0024 · regional, not allelic
Overall
CADD	20.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.111% East Asian · 50/44,878 alleles

Filtering AF 0.0867% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0781%

Overall 0.0101% 163/1,613,500 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.111%	898
South Asian	0.0516%	1,938
Remaining individualsnot grpmax-eligible	0.0192%	5,208
African / African-American	0.00933%	10,720
European (non-Finnish)	0.00398%	25,105

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: CCDC183
Protein: p.Arg237Gln
Coding: c.710G>A
MANE Select: NM_001039374
dbSNP: rs201155882
Type: single nucleotide variant
Location: chr9:136804545 (GRCh38)
Gene constraint: LOEUF 1.225 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.98

Full CCDC183 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC183 p.Arg237Gly Uncertain significance ★ ⚠ same residue
CCDC183 p.Gln296Ter Likely pathogenic ★ same type
CCDC183 p.Ala238Thr Uncertain significance ★ ⚠ same type
CCDC183 p.Ala348Thr Uncertain significance ★ ⚠ same type
CCDC183 p.Ala392Val Uncertain significance ★ ⚠ same type
CCDC183 p.Ala424Glu Uncertain significance ★ ⚠ same type
CCDC183 p.Ala518Thr Uncertain significance ★ ⚠ same type
CCDC183 p.Arg117Pro Uncertain significance ★ ⚠ 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/ccdc183-p-arg237gln (accessed [today's date]).

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