Is KDM5B p.Asp1012= (c.3036C>T) pathogenic?

KDM5B p.Asp1012= (c.3036C>T) is classified Likely benign in KDM5B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-17). Ultra-rare (popmax 0.0198%, sas); Associated with KDM5B-related disorder.

What condition is associated with KDM5B p.Asp1012= (c.3036C>T)?

KDM5B p.Asp1012= (c.3036C>T) is associated with KDM5B-related disorder (ClinVar).

How common is KDM5B p.Asp1012= (c.3036C>T) in the general population?

KDM5B p.Asp1012= (c.3036C>T) is ultra-rare (popmax 0.0198%, sas) (gnomAD).

KDM5B p.Asp1012=

c.3036C>T · rs769873701 · VCV3041398

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0198%, sas)

Conditions

KDM5B-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 0.8	GERP 0.97, phastCons 1
Overall
CADD	8.656	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0198% South Asian · 18/91,040 alleles

Filtering AF 0.0127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.00118% 19/1,612,780 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0198%	5,058
European (non-Finnish)	8.47e-05%	1,179,947

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: KDM5B
Protein: p.Asp1012=
Coding: c.3036C>T
MANE Select: NM_006618
dbSNP: rs769873701
Type: single nucleotide variant
Location: chr1:202740722 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.52 · 56 PDB
Residue 1012: a UniProt-annotated variant site (in mrt65)

Full KDM5B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

KDM5B-related disorder

Similar variants

KDM5B p.Arg1214Ter Likely pathogenic ★★ same condition
KDM5B p.Arg1253Ter Pathogenic/Likely pathogenic ★★ same condition
KDM5B c.4022-1G>C Likely pathogenic ★ same condition
KDM5B p.Gln1182Ter Likely pathogenic ★ same condition
KDM5B p.Ser1312Ter Likely pathogenic ★ same condition
KDM5B p.Pro163Leu Uncertain significance ★ ⚠ same condition
KDM5B p.Gln106Ter Likely pathogenic same condition
KDM5B c.204+5G>T Uncertain significance 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/kdm5b-p-asp1012 (accessed [today's date]).

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