Is KDM1A p.Asp331= (c.993T>C) pathogenic?

KDM1A p.Asp331= (c.993T>C) is classified Likely benign in KDM1A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-29). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with KDM1A p.Asp331= (c.993T>C)?

KDM1A p.Asp331= (c.993T>C) is associated with Inborn genetic diseases (ClinVar).

How common is KDM1A p.Asp331= (c.993T>C) in the general population?

KDM1A p.Asp331= (c.993T>C) is absent from gnomAD v4.1 (gnomAD).

KDM1A p.Asp331=

c.993T>C · VCV4091036

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

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 1.9	GERP 0.42, phastCons 1
Overall
CADD	13.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: KDM1A
Protein: p.Asp331=
Coding: c.993T>C
MANE Select: NM_001009999
Type: single nucleotide variant
Location: chr1:23057486 (GRCh38)
Gene constraint: LOEUF 0.638 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.29 · 129 PDB
Residue 331: the 'demethylase activity' region; a UniProt-annotated variant site (in aimah3; likely pathogenic; loss of protein expression in patient adrenal samples)

Full KDM1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KDM1A p.Ala10Val Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala11Ser Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala11Thr Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala12Val Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala13Thr Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala18Thr Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala197Thr Uncertain significance ★★ ⚠ same condition
KDM1A p.Ala558Gly 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/kdm1a-p-asp331 (accessed [today's date]).

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