Is CIC p.Ala2056fs (c.6166_6167del) pathogenic?

CIC p.Ala2056fs (c.61666167del) is classified Pathogenic in CIC (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-22). Absent from gnomAD; Associated with intellectual developmental disorder, autosomal dominant 45.

What condition is associated with CIC p.Ala2056fs (c.6166_6167del)?

CIC p.Ala2056fs (c.6166_6167del) is associated with intellectual developmental disorder, autosomal dominant 45 (ClinVar).

How common is CIC p.Ala2056fs (c.6166_6167del) in the general population?

CIC p.Ala2056fs (c.6166_6167del) is absent from gnomAD (gnomAD).

CIC p.Ala2056fs

c.6166_6167del · rs2147313207 · VCV1301400

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual developmental disorder, autosomal dominant 45

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.3	GERP -3.4
Region caveats
Repeat context	tandem	(CCAGCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CIC
Protein: p.Ala2056fs
Coding: c.6166_6167del
MANE Select: NM_005984 · reported on NM_001386298
dbSNP: rs2147313207
Type: Deletion
Location: chr19:42292829 (GRCh38)
Structure: AlphaFold pLDDT 75.09

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

Disease context

intellectual developmental disorder, autosomal dominant 45 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CIC p.Pro788fs Pathogenic/Likely pathogenic ★★ same condition
CIC p.Ala1694fs Likely pathogenic ★ same condition
CIC p.Ala1809fs Likely pathogenic ★ same condition
CIC p.Asp38fs Likely pathogenic ★ same condition
CIC p.Gln2115fs Likely pathogenic ★ same condition
CIC p.Gln894fs Likely pathogenic ★ same condition
CIC p.Glu103fs Likely pathogenic ★ same condition
CIC p.Gly544fs Likely pathogenic ★ 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-ala2056fs (accessed [today's date]).

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