Is KDM2B p.Ser233= (c.699C>T) pathogenic?

KDM2B p.Ser233= (c.699C>T) is classified Likely benign in KDM2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-02-26). Very rare (popmax 0.00668%, afr); Associated with KDM2B-related disorder.

What condition is associated with KDM2B p.Ser233= (c.699C>T)?

KDM2B p.Ser233= (c.699C>T) is associated with KDM2B-related disorder (ClinVar).

How common is KDM2B p.Ser233= (c.699C>T) in the general population?

KDM2B p.Ser233= (c.699C>T) is very rare (popmax 0.00668%, afr) (gnomAD).

KDM2B p.Ser233=

c.699C>T · rs200066174 · VCV3051672

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, afr)

Conditions

KDM2B-related disorder

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 -0.62	GERP -3.7
Overall
CADD	11.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% African / African-American · 5/74,886 alleles

Filtering AF 0.00286% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00195%

Overall 0.00273% 44/1,613,366 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00668%	14,977
South Asian	0.00659%	15,177
European (non-Finnish)	0.0028%	35,742

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: KDM2B
Protein: p.Ser233=
Coding: c.699C>T
MANE Select: NM_032590
dbSNP: rs200066174
Type: single nucleotide variant
Location: chr12:121534575 (GRCh38)
Gene constraint: LOEUF 0.266 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.20 · 4 PDB
Residue 233: the jmjc domain

Full KDM2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

KDM2B-related disorder

Similar variants

KDM2B p.Arg614Pro Pathogenic/Likely pathogenic ★★ same condition
KDM2B p.Cys616Arg Pathogenic/Likely pathogenic ★★ same condition
KDM2B c.778-2A>G Likely pathogenic ★ same condition
KDM2B p.Cys627Ser Pathogenic ★ same condition
KDM2B p.Glu896Ter Uncertain significance ★ same condition
KDM2B p.Gly789Ser Uncertain significance ★ ⚠ same condition
KDM2B p.His781Arg Uncertain significance ★ ⚠ same condition
KDM2B p.Arg167Gln 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/kdm2b-p-ser233 (accessed [today's date]).

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