Is DNAH7 p.Pro2490= (c.7470T>A) pathogenic?

DNAH7 p.Pro2490= (c.7470T>A) is classified Likely benign in DNAH7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-03-11). Absent from gnomAD v4.1; Associated with DNAH7-related disorder.

What condition is associated with DNAH7 p.Pro2490= (c.7470T>A)?

DNAH7 p.Pro2490= (c.7470T>A) is associated with DNAH7-related disorder (ClinVar).

How common is DNAH7 p.Pro2490= (c.7470T>A) in the general population?

DNAH7 p.Pro2490= (c.7470T>A) is absent from gnomAD v4.1 (gnomAD).

DNAH7 p.Pro2490=

c.7470T>A · VCV3351729

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

DNAH7-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 -0.76	GERP -3.8
Overall
CADD	1.846	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: DNAH7
Protein: p.Pro2490=
Coding: c.7470T>A
MANE Select: NM_018897
Type: single nucleotide variant
Location: chr2:195864185 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Residue 2490: the 'aaa 4' region

Full DNAH7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAH7-related disorder

Similar variants

DNAH7 p.Glu3626= Uncertain significance ★ same condition
DNAH7 p.Val827Ile Uncertain significance ★ ⚠ same condition
DNAH7 p.Ala1739Thr Uncertain significance ⚠ same condition
DNAH7 p.Arg691Trp Uncertain significance ⚠ same condition
DNAH7 c.1173+4A>C Likely benign same condition
DNAH7 c.6118-10T>G Likely benign same condition
DNAH7 c.7507-6A>T Likely benign same condition
DNAH7 c.*9C>T Likely 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/dnah7-p-pro2490 (accessed [today's date]).

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