Is DNAH8 p.Pro4361Leu (c.13082C>T) pathogenic?

DNAH8 p.Pro4361Leu (c.13082C>T) is classified Uncertain significance in DNAH8 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-01). AlphaMissense: likely benign (0.1432); Ultra-rare (popmax 0.0188%, sas); Associated with spermatogenic failure 46.

What condition is associated with DNAH8 p.Pro4361Leu (c.13082C>T)?

DNAH8 p.Pro4361Leu (c.13082C>T) is associated with spermatogenic failure 46 (ClinVar).

How common is DNAH8 p.Pro4361Leu (c.13082C>T) in the general population?

DNAH8 p.Pro4361Leu (c.13082C>T) is ultra-rare (popmax 0.0188%, sas) (gnomAD).

What do computational predictors say about DNAH8 p.Pro4361Leu (c.13082C>T)?

AlphaMissense predicts likely benign (score 0.1432) — an in-silico prediction, not a clinical call.

DNAH8 p.Pro4361Leu

c.13082C>T · rs770419203 · VCV2440921

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1432 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0188%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

spermatogenic failure 46

Computational evidence

Protein change
AlphaMissense	0.1432	likely benign
REVEL	0.105	moderately 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 4.8	GERP 2.3, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 112 kb · p 0.0022 · regional, not allelic
Overall
CADD	19.14	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P4144L vs ClinVar P4361L) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0188% South Asian · 17/90,236 alleles

Filtering AF 0.0119% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00984%

Overall 0.00562% 90/1,600,166 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0188%	5,308
Admixed American	0.0168%	5,943
Remaining individualsnot grpmax-eligible	0.00968%	10,333
European (non-Finnish)	0.00471%	21,251
African / African-American	0.00268%	37,277

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: DNAH8
Protein: p.Pro4361Leu
Coding: c.13082C>T
MANE Select: NM_001206927
dbSNP: rs770419203
Type: single nucleotide variant
Location: chr6:38990040 (GRCh38)
Gene constraint: LOEUF 0.692 · pLI <0.01 (gnomAD)
Residue 4361: a UniProt-annotated variant site (found in a patient with primary ciliary dyskinesia; uncertain significance)

Full DNAH8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spermatogenic failure 46 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DNAH8 p.Pro4361= Likely benign ★★ same residue
DNAH8 c.10963-1G>A Likely pathogenic ★★ same condition
DNAH8 c.2664+2T>C Likely pathogenic ★★ same condition
DNAH8 c.5734-1G>T Likely pathogenic ★★ same condition
DNAH8 p.Arg1090Ter Pathogenic/Likely pathogenic ★★ same condition
DNAH8 p.Arg207Ter Pathogenic/Likely pathogenic ★★ same condition
DNAH8 p.Arg4166Ter Pathogenic/Likely pathogenic ★★ same condition
DNAH8 p.Arg1126His Uncertain significance ★★ ⚠ 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/dnah8-p-pro4361leu (accessed [today's date]).

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