Is CIC p.Ala2463Ser (c.7387G>T) pathogenic?

CIC p.Ala2463Ser (c.7387G>T) is classified Uncertain significance in CIC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-28). AlphaMissense: likely benign (0.0824); Very rare (popmax 0.0039%, amr); Associated with Inborn genetic diseases.

What condition is associated with CIC p.Ala2463Ser (c.7387G>T)?

CIC p.Ala2463Ser (c.7387G>T) is associated with Inborn genetic diseases (ClinVar).

How common is CIC p.Ala2463Ser (c.7387G>T) in the general population?

CIC p.Ala2463Ser (c.7387G>T) is very rare (popmax 0.0039%, amr) (gnomAD).

What do computational predictors say about CIC p.Ala2463Ser (c.7387G>T)?

AlphaMissense predicts likely benign (score 0.0824) — an in-silico prediction, not a clinical call.

CIC p.Ala2463Ser

c.7387G>T · rs762480443 · VCV3144973

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0824 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0039%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0824	likely benign
REVEL	0.069	moderately benign-leaning
SaProt	LLR -6.39	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 6.3	GERP -2.4, phastCons 1
Overall
CADD	19.93	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM A1554S vs ClinVar A2463S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0039% Admixed American · 2/51,298 alleles

Filtering AF 0.000646% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000242%

Overall 0.000523% 8/1,530,232 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0039%	25,649
Remaining individualsnot grpmax-eligible	0.00165%	60,580
European (non-Finnish)	0.000434%	230,165

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.Ala2463Ser
Coding: c.7387G>T
MANE Select: NM_005984 · reported on NM_001386298
dbSNP: rs762480443
Type: single nucleotide variant
Location: chr19:42295024 (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

Similar variants

CIC p.Ala2463Thr Uncertain significance ★★ ⚠ same residue
CIC c.2795-2056C>T Uncertain significance ★★ ⚠ same condition
CIC p.Ala1228Val Uncertain significance ★★ ⚠ same condition
CIC p.Ala1445Gly Uncertain significance ★★ ⚠ same condition
CIC p.Ala1750Val Uncertain significance ★★ ⚠ same condition
CIC p.Ala1975Gly Uncertain significance ★★ ⚠ same condition
CIC p.Arg1205Trp Uncertain significance ★★ ⚠ same condition
CIC p.Arg1481Gln 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-ala2463ser (accessed [today's date]).

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