Is DNAH3 p.Val3634Phe (c.10900G>T) pathogenic?

DNAH3 p.Val3634Phe (c.10900G>T) is classified Likely benign in DNAH3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-01). AlphaMissense: likely benign (0.2935); Rare (popmax 0.531%, nfe).

How common is DNAH3 p.Val3634Phe (c.10900G>T) in the general population?

DNAH3 p.Val3634Phe (c.10900G>T) is rare (popmax 0.531%, nfe) (gnomAD).

What do computational predictors say about DNAH3 p.Val3634Phe (c.10900G>T)?

AlphaMissense predicts likely benign (score 0.2935) — an in-silico prediction, not a clinical call.

DNAH3 p.Val3634Phe

c.10900G>T · rs142557616 · VCV2646287

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2935 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.531%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.2935	likely benign
REVEL	0.205	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.95	GERP -5.9, phastCons 0.002
Overall
CADD	14.42	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V3680F vs ClinVar V3634F) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.531% European (non-Finnish) · 6,267/1,180,010 alleles

Filtering AF 0.52% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.516%

Overall 0.55% 8,880/1,614,130 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.86%	54
Finnishnot grpmax-eligible	1.59%	63
Remaining individualsnot grpmax-eligible	0.643%	155
European (non-Finnish)grpmax	0.531%	188
Middle Eastern	0.511%	196
South Asian	0.43%	232
Admixed American	0.262%	382
African / African-American	0.0826%	1,210
East Asian	0.00446%	22,441

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DNAH3
Protein: p.Val3634Phe
Coding: c.10900G>T
MANE Select: NM_001347886
dbSNP: rs142557616
Type: single nucleotide variant
Location: chr16:20954846 (GRCh38)
Gene constraint: LOEUF 0.834 · pLI <0.01 (gnomAD)
Residue 3634: the 'aaa 6' region; a UniProt-annotated variant site (found in a male with oligoasthenoteratozoospermia; uncertain significance; severely impaired sperm motility; multiple morphological abnormalities of the sperm flagella; partial loss and disintegration of the flagellar axoneme, accompanied by damage to the mitochondrial sheath); a UniProt-annotated variant site (found in a male with asthenoteratozoospermia; uncertain significance; severely impaired sperm motility; multiple morphological abnormalities of the sperm flagella; disorganization of flagellar components, notably inner dynein arms); a UniProt-annotated variant site (found in a male with oligoasthenoteratozoospermia; uncertain significance; severely impaired sperm motility; multiple morphological abnormalities of the sperm flagella; disorganization of the flagellar axoneme ultrastructure, including abnormalities in the inner dynein arms, mitochondrial sheath and fibrous sheath)

Full DNAH3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAH3 p.Ala1918Gly Uncertain significance ★★ ⚠ same type
DNAH3 p.Arg1228Gln Uncertain significance ★★ same type
DNAH3 p.Arg635Gln Uncertain significance ★★ same type
DNAH3 p.Asn1728Ser Uncertain significance ★★ ⚠ same type
DNAH3 p.Asp3656Asn Uncertain significance ★★ same type
DNAH3 p.Leu2597Val Uncertain significance ★★ same type
DNAH3 p.Leu4044Phe Uncertain significance ★★ ⚠ same type
DNAH3 p.Lys374Gln Uncertain significance ★★ ⚠ 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/dnah3-p-val3634phe (accessed [today's date]).

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