Is JMJD1C p.Asp1069= (c.3207T>C) pathogenic?

JMJD1C p.Asp1069= (c.3207T>C) is classified Likely benign in JMJD1C (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-22). Absent from gnomAD v4.1; Associated with Early Myoclonic Encephalopathy.

What condition is associated with JMJD1C p.Asp1069= (c.3207T>C)?

JMJD1C p.Asp1069= (c.3207T>C) is associated with Early Myoclonic Encephalopathy (ClinVar).

How common is JMJD1C p.Asp1069= (c.3207T>C) in the general population?

JMJD1C p.Asp1069= (c.3207T>C) is absent from gnomAD v4.1 (gnomAD).

JMJD1C p.Asp1069=

c.3207T>C · rs1461358577 · VCV1117005

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Early Myoclonic Encephalopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1	GERP -2.2, phastCons 0.014
Overall
CADD	3.051	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: JMJD1C
Protein: p.Asp1069=
Coding: c.3207T>C
MANE Select: NM_032776
dbSNP: rs1461358577
Type: single nucleotide variant
Location: chr10:63208462 (GRCh38)
Gene constraint: LOEUF 0.157 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 50.01 · 3 PDB

Full JMJD1C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Early Myoclonic Encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

JMJD1C p.Asp1069Glu Uncertain significance ★ ⚠ same residue
JMJD1C p.Ala1128Val Uncertain significance ★★ ⚠ same condition
JMJD1C p.Ala1337Ser Uncertain significance ★★ ⚠ same condition
JMJD1C p.Ala1618Thr Uncertain significance ★★ ⚠ same condition
JMJD1C p.Ala2276Thr Uncertain significance ★★ ⚠ same condition
JMJD1C p.Ala23Thr Uncertain significance ★★ ⚠ same condition
JMJD1C p.Ala23Val Uncertain significance ★★ ⚠ same condition
JMJD1C p.Ala2Thr 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/jmjd1c-p-asp1069 (accessed [today's date]).

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