Is DNAH10 p.Pro1643= (c.4929C>T) pathogenic?

DNAH10 p.Pro1643= (c.4929C>T) is classified Likely benign in DNAH10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-20). Ultra-rare (popmax 0.0657%, mid); Associated with DNAH10-related disorder.

What condition is associated with DNAH10 p.Pro1643= (c.4929C>T)?

DNAH10 p.Pro1643= (c.4929C>T) is associated with DNAH10-related disorder (ClinVar).

How common is DNAH10 p.Pro1643= (c.4929C>T) in the general population?

DNAH10 p.Pro1643= (c.4929C>T) is ultra-rare (popmax 0.0657%, mid) (gnomAD).

DNAH10 p.Pro1643=

c.4929C>T · rs58292766 · VCV3039498

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0657%, mid)

Conditions

DNAH10-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 -20	GERP -3.8
Overall
CADD	0.17	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0657% Middle Eastern · 4/6,084 alleles

Filtering AF 0.0246% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0214%

Overall 0.00638% 103/1,613,716 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0657%	1,521
South Asian	0.034%	2,938
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,802
European (non-Finnish)	0.00517%	19,342
Remaining individualsnot grpmax-eligible	0.0048%	20,820
Admixed American	0.00333%	29,996

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: DNAH10
Protein: p.Pro1643=
Coding: c.4929C>T
MANE Select: NM_001372106
dbSNP: rs58292766
Type: single nucleotide variant
Location: chr12:123838482 (GRCh38)
Gene constraint: LOEUF 0.763 · pLI <0.01 (gnomAD)
Residue 1643: the 'stem' region

Full DNAH10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAH10-related disorder

Similar variants

DNAH10 p.Pro3309Ala Uncertain significance ★ ⚠ same condition
DNAH10 p.Gln999Glu Uncertain significance ⚠ same condition
DNAH10 p.Lys132Asn Uncertain significance ⚠ same condition
DNAH10 c.11766+6C>T Likely benign same condition
DNAH10 c.2987+8C>T Likely benign same condition
DNAH10 p.Ala1801= Benign same condition
DNAH10 p.Ala2444= Likely benign same condition
DNAH10 p.Arg3494= 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/dnah10-p-pro1643 (accessed [today's date]).

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