Is CIC p.Arg1331Gln (c.3992G>A) pathogenic?

CIC p.Arg1331Gln (c.3992G>A) is classified Conflicting classifications of pathogenicity in CIC (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-11-09). AlphaMissense: likely benign (0.1383); Ultra-rare (popmax 0.0331%, mid); Associated with Inborn genetic diseases.

What condition is associated with CIC p.Arg1331Gln (c.3992G>A)?

CIC p.Arg1331Gln (c.3992G>A) is associated with Inborn genetic diseases, intellectual developmental disorder, autosomal dominant 45 (ClinVar).

How common is CIC p.Arg1331Gln (c.3992G>A) in the general population?

CIC p.Arg1331Gln (c.3992G>A) is ultra-rare (popmax 0.0331%, mid) (gnomAD).

What do computational predictors say about CIC p.Arg1331Gln (c.3992G>A)?

AlphaMissense predicts likely benign (score 0.1383) — an in-silico prediction, not a clinical call.

CIC p.Arg1331Gln

c.3992G>A · rs779676461 · VCV2440081

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1383 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0331%, mid)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1383	likely benign
REVEL	0.263	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.4, phastCons 1
Overall
CADD	25.9	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R422Q vs ClinVar R1331Q) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0331% Middle Eastern · 2/6,036 alleles

Filtering AF 0.00834% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00776%

Overall 0.00781% 126/1,613,908 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0331%	3,018
European (non-Finnish)	0.00983%	10,172
Admixed American	0.00667%	14,999
Remaining individualsnot grpmax-eligible	0.0032%	31,239
African / African-American	0.00267%	37,466

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: CIC
Protein: p.Arg1331Gln
Coding: c.3992G>A
MANE Select: NM_005984 · reported on NM_001386298
dbSNP: rs779676461
Type: single nucleotide variant
Location: chr19:42289311 (GRCh38)
Structure: AlphaFold pLDDT 75.09

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: intellectual developmental disorder, autosomal dominant 45

Similar variants

CIC p.Arg1331Gly Uncertain significance ★ ⚠ same residue
CIC c.3179+1G>T Pathogenic ★★ same condition
CIC c.5903-2A>G Likely pathogenic ★★ same condition
CIC p.Asn1136Ser Likely pathogenic ★★ same condition
CIC p.Gln1134Ter Pathogenic ★★ same condition
CIC p.Gln1799Ter Likely pathogenic ★★ same condition
CIC c.2795-2056C>T Uncertain significance ★★ same condition
CIC p.Ala1228Val 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/cic-p-arg1331gln (accessed [today's date]).

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