Is DNMBP p.Lys1009= (c.3027G>A) pathogenic?

DNMBP p.Lys1009= (c.3027G>A) is classified Likely benign in DNMBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-22). Very rare (popmax 6.84e-05%); Associated with DNMBP-related disorder.

What condition is associated with DNMBP p.Lys1009= (c.3027G>A)?

DNMBP p.Lys1009= (c.3027G>A) is associated with DNMBP-related disorder (ClinVar).

How common is DNMBP p.Lys1009= (c.3027G>A) in the general population?

DNMBP p.Lys1009= (c.3027G>A) is very rare (popmax 6.84e-05%) (gnomAD).

DNMBP p.Lys1009=

c.3027G>A · rs2493139786 · VCV3046632

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.84e-05%)

Conditions

DNMBP-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 0.43	GERP -1.5, phastCons 0.99
Overall
CADD	7.452	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.84e-05%

Overall 6.84e-05% 1/1,461,854 alleles · very rare

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: DNMBP
Protein: p.Lys1009=
Coding: c.3027G>A
MANE Select: NM_015221
dbSNP: rs2493139786
Type: single nucleotide variant
Location: chr10:99896291 (GRCh38)
Gene constraint: LOEUF 0.664 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.91 · 7 PDB
Residue 1009: a UniProt-annotated variant site (in ctrct48); the bar domain

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

Disease context

DNMBP-related disorder

Similar variants

DNMBP c.2261-21460G>A Uncertain significance ★ same condition
DNMBP c.2261-20475C>G Benign same condition
DNMBP c.2261-20486G>A Benign same condition
DNMBP c.2261-20487C>T Benign same condition
DNMBP c.2261-20815A>G Benign same condition
DNMBP c.2261-21193G>A Benign same condition
DNMBP c.2261-21218G>A Benign same condition
DNMBP c.2261-21476T>C Benign 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/dnmbp-p-lys1009 (accessed [today's date]).

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