Is CNBP p.Cys77= (c.231C>T) pathogenic?

CNBP p.Cys77= (c.231C>T) is classified Likely benign in CNBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-30). Very rare (popmax 0.00267%, afr); Associated with CNBP-related disorder.

What condition is associated with CNBP p.Cys77= (c.231C>T)?

CNBP p.Cys77= (c.231C>T) is associated with CNBP-related disorder (ClinVar).

How common is CNBP p.Cys77= (c.231C>T) in the general population?

CNBP p.Cys77= (c.231C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

CNBP p.Cys77=

c.231C>T · rs767954262 · VCV3044454

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

CNBP-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.134	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP -2.4, phastCons 1
Overall
CADD	14.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,920 alleles

Filtering AF 0.000878% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000717%

Overall 0.00149% 24/1,614,046 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0048%	20,829
African / African-Americangrpmax	0.00267%	37,460
Admixed American	0.00167%	60,002
Finnishnot grpmax-eligible	0.00156%	64,018
European (non-Finnish)	0.00144%	69,414

Remaining individuals 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: CNBP
Protein: p.Cys77=
Coding: c.231C>T
MANE Select: NM_003418
dbSNP: rs767954262
Type: single nucleotide variant
Location: chr3:129171264 (GRCh38)
Gene constraint: LOEUF 0.541 · pLI 0.95 (gnomAD)
Structure: AlphaFold pLDDT 71.09

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

Disease context

CNBP-related disorder

Similar variants

CNBP c.-14-963A>T Likely benign same condition
CNBP c.-14-837_-14-830del Likely benign same condition
CNBP c.-14-853_-14-838del Likely benign same condition
CNBP c.-14-857_-14-838del Likely benign same condition
CNBP c.-14-962GT[18] Likely benign same condition
CNBP p.Asp52= Benign ★★ same type
CNBP p.Asn100Ser Uncertain significance ★ ⚠ same type
CNBP p.Asp52Glu 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/cnbp-p-cys77 (accessed [today's date]).

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