Is DYNLT4 p.Arg29Pro (c.86G>C) pathogenic?

DYNLT4 p.Arg29Pro (c.86G>C) is classified Likely benign in DYNLT4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-12). AlphaMissense: likely benign (0.0625); Ultra-rare (popmax 0.0146%, afr).

How common is DYNLT4 p.Arg29Pro (c.86G>C) in the general population?

DYNLT4 p.Arg29Pro (c.86G>C) is ultra-rare (popmax 0.0146%, afr) (gnomAD).

What do computational predictors say about DYNLT4 p.Arg29Pro (c.86G>C)?

AlphaMissense predicts likely benign (score 0.0625) — an in-silico prediction, not a clinical call.

DYNLT4 p.Arg29Pro

c.86G>C · rs750113722 · VCV3086587

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0625 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0146%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0625	likely benign
REVEL	0.03	moderately benign-leaning
SaProt	LLR -6.32	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.98	GERP -2.1
Regional constraint	o/e 1.01	unconstrained · MANE · 662 bp · p 0.79 · regional, not allelic
Overall
CADD	14.11	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0146% African / African-American · 10/68,272 alleles

Filtering AF 0.00788% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00598%

Overall 0.000738% 11/1,490,912 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0146%	6,827
South Asian	0.00129%	77,288

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: DYNLT4
Protein: p.Arg29Pro
Coding: c.86G>C
MANE Select: NM_001377534
dbSNP: rs750113722
Type: single nucleotide variant
Location: chr1:44806583 (GRCh38)
Gene constraint: LOEUF 1.943 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.02
Residue 29: the 'disordered' region

Full DYNLT4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNLT4 p.Arg29Gln Uncertain significance ★ ⚠ same residue
DYNLT4 p.Ala130Ser Uncertain significance ★ ⚠ same type
DYNLT4 p.Ala146Thr Uncertain significance ★ ⚠ same type
DYNLT4 p.Ala146Val Uncertain significance ★ ⚠ same type
DYNLT4 p.Ala195Val Uncertain significance ★ ⚠ same type
DYNLT4 p.Ala41Ser Uncertain significance ★ ⚠ same type
DYNLT4 p.Ala58Thr Uncertain significance ★ ⚠ same type
DYNLT4 p.Ala72Thr 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/dynlt4-p-arg29pro (accessed [today's date]).

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