Is CIB2 p.Asp159= (c.477C>T) pathogenic?

CIB2 p.Asp159= (c.477C>T) is classified Benign in CIB2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-06-28). Common (popmax 24.9%, nfe) — too common for a highly-penetrant pathogenic allele.

CIB2 p.Asp159=

Q: How common is CIB2 p.Asp159= (c.477C>T) in the general population?

CIB2 p.Asp159= (c.477C>T) is common (popmax 24.9%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.477C>T · rs10456 · VCV226517

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 24.9%, nfe) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP -6.6	GERP -3.4
Overall
CADD	0.26	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 24.9% European (non-Finnish) · 293,427/1,179,950 alleles

Filtering AF 24.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 24.8%

Overall 22.8% 368,236/1,614,016 alleles · common

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	30.5%	3
Ashkenazi Jewishnot grpmax-eligible	28.8%	3
European (non-Finnish)grpmax	24.9%	4
Remaining individualsnot grpmax-eligible	22.3%	4
Middle Eastern	22.1%	5
Amishnot grpmax-eligible	17%	6
Admixed American	16.6%	6
South Asian	16.2%	6
African / African-American	7.54%	13
East Asian	2.24%	45

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CIB2
Protein: p.Asp159=
Coding: c.477C>T
MANE Select: NM_006383
dbSNP: rs10456
Type: single nucleotide variant
Location: chr15:78105804 (GRCh38)
Gene constraint: LOEUF 1.274 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.71 · 1 PDB
Residue 159: a UniProt-annotated variant site (in dfnb48); a UniProt-annotated variant site (in dfnb48; uncertain significance); the ef-hand 3 domain; a β-strand; a binding site

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

Similar variants

CIB2 p.Asp159fs Pathogenic same residue
CIB2 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same type
CIB2 p.Arg33Ter Pathogenic ★★ same type
CIB2 p.Arg66Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
CIB2 c.198+3A>G Uncertain significance ★★ same type
CIB2 p.Ala108Thr Uncertain significance ★★ ⚠ same type
CIB2 p.Ala76Val Uncertain significance ★★ ⚠ same type
CIB2 p.Arg134Gln 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/cib2-p-asp159 (accessed [today's date]).

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