Is DNAH2 p.Leu1024= (c.3072G>A) pathogenic?

DNAH2 p.Leu1024= (c.3072G>A) is classified Likely benign in DNAH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-01). Absent from gnomAD v4.1.

How common is DNAH2 p.Leu1024= (c.3072G>A) in the general population?

DNAH2 p.Leu1024= (c.3072G>A) is absent from gnomAD v4.1 (gnomAD).

DNAH2 p.Leu1024=

c.3072G>A · VCV3389743

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 6.5	GERP 1.1, phastCons 1
Overall
CADD	10.38	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: DNAH2
Protein: p.Leu1024=
Coding: c.3072G>A
MANE Select: NM_020877
Type: single nucleotide variant
Location: chr17:7763924 (GRCh38)
Gene constraint: LOEUF 0.655 · pLI <0.01 (gnomAD)
Residue 1024: the 'stem' region

Full DNAH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAH2 p.Ala1036Val Uncertain significance ★★ ⚠ same type
DNAH2 p.Arg1533Cys Uncertain significance ★★ ⚠ same type
DNAH2 p.Arg2538Gln Uncertain significance ★★ same type
DNAH2 p.Arg3759His Uncertain significance ★★ ⚠ same type
DNAH2 p.Gln2069Glu Uncertain significance ★★ same type
DNAH2 p.Ile4043Ser Uncertain significance ★★ ⚠ same type
DNAH2 p.Pro3819Leu Uncertain significance ★★ ⚠ same type
DNAH2 c.10169+3G>A Benign ★★ same type

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/dnah2-p-leu1024 (accessed [today's date]).

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