Is CIB2 p.Lys4Ter (c.10A>T) pathogenic?

CIB2 p.Lys4Ter (c.10A>T) is classified Likely pathogenic in CIB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-06). Absent from gnomAD v4.1; Associated with CIB2-related disorders.

What condition is associated with CIB2 p.Lys4Ter (c.10A>T)?

CIB2 p.Lys4Ter (c.10A>T) is associated with CIB2-related disorders (ClinVar).

How common is CIB2 p.Lys4Ter (c.10A>T) in the general population?

CIB2 p.Lys4Ter (c.10A>T) is absent from gnomAD v4.1 (gnomAD).

CIB2 p.Lys4Ter

c.10A>T · VCV4926088

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CIB2-related disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 6
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.7, phastCons 1
Overall
CADD	43.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CIB2
Protein: p.Lys4Ter
Coding: c.10A>T
MANE Select: NM_006383
Type: single nucleotide variant
Location: chr15:78131206 (GRCh38)
Gene constraint: LOEUF 1.274 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.71 · 1 PDB

Full CIB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CIB2-related disorders

Similar variants

CIB2 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same condition
CIB2 p.Arg33Ter Pathogenic ★★ same condition
CIB2 c.198+1G>A Likely pathogenic ★ same condition
CIB2 c.199-125G>A Likely pathogenic ★ same condition
CIB2 p.Arg186Trp Conflicting classifications of pathogenicity ★ ⚠ same condition
CIB2 p.Lys151Asn Conflicting classifications of pathogenicity ★ ⚠ same condition
CIB2 c.199-34C>T Likely benign same condition
CIB2 p.Glu100fs Pathogenic/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/cib2-p-lys4ter (accessed [today's date]).

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