Is CTBP2 p.Ser164= (c.492C>T) pathogenic?

CTBP2 p.Ser164= (c.492C>T) is classified Likely benign in CTBP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-01). Rare (popmax 0.116%, mid).

How common is CTBP2 p.Ser164= (c.492C>T) in the general population?

CTBP2 p.Ser164= (c.492C>T) is rare (popmax 0.116%, mid) (gnomAD).

CTBP2 p.Ser164=

c.492C>T · rs372293905 · VCV2640952

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.116%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3	GERP -4.8
Overall
CADD	11.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.116% Middle Eastern · 7/6,042 alleles

Filtering AF 0.0601% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0544%

Overall 0.0107% 173/1,613,330 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.116%	863
African / African-American	0.0759%	1,317
Remaining individualsnot grpmax-eligible	0.0192%	5,207
Admixed American	0.0133%	7,500
South Asian	0.0132%	7,589
European (non-Finnish)	0.00644%	15,526
Finnishnot grpmax-eligible	0.00158%	63,310

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: CTBP2
Protein: p.Ser164=
Coding: c.492C>T
MANE Select: NM_001329
dbSNP: rs372293905
Type: single nucleotide variant
Location: chr10:124998037 (GRCh38)
Gene constraint: LOEUF 0.522 · pLI 0.82 (gnomAD)
Structure: AlphaFold pLDDT 83.67 · 5 PDB

Full CTBP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTBP2 c.58+11873C>T Benign ★★ same type
CTBP2 c.58+11963C>T Benign ★★ same type
CTBP2 c.58+12441C>T Benign ★★ same type
CTBP2 c.58+12475A>C Benign ★★ same type
CTBP2 p.Pro309= Benign ★★ same type
ZRANB1 p.Arg669Trp Uncertain significance ★ ⚠ same type
ZRANB1 p.Arg670Trp Uncertain significance ★ ⚠ same type
ZRANB1 p.Arg688Gln 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/ctbp2-p-ser164 (accessed [today's date]).

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