Is DYNLT3 p.Ala61= (c.183C>T) pathogenic?

DYNLT3 p.Ala61= (c.183C>T) is classified Benign in DYNLT3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2016-03-29). Common (popmax 65.2%, afr) — too common for a highly-penetrant pathogenic allele.

DYNLT3 p.Ala61=

Q: How common is DYNLT3 p.Ala61= (c.183C>T) in the general population?

DYNLT3 p.Ala61= (c.183C>T) is common (popmax 65.2%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.183C>T · rs11771 · VCV402816

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 65.2%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.2	GERP -2.7, phastCons 1
Overall
CADD	4.097	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 65.2% African / African-American · 36,482/55,962 alleles

Filtering AF 64.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 64.4%

Overall 19% 221,987/1,169,836 alleles · common exomes 188,160/1,059,891 · genomes 33,827/109,945 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	65.2%	2
East Asian	26.5%	4
South Asian	24.9%	4
Middle Eastern	22.7%	4
Admixed American	21.4%	5
Remaining individualsnot grpmax-eligible	19.7%	5
Finnishnot grpmax-eligible	19.2%	5
Amishnot grpmax-eligible	16.4%	6
European (non-Finnish)	15.3%	7
Ashkenazi Jewishnot grpmax-eligible	14.4%	7

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: DYNLT3
Protein: p.Ala61=
Coding: c.183C>T
MANE Select: NM_006520
dbSNP: rs11771
Type: single nucleotide variant
Location: chrX:37841795 (GRCh38)
Structure: AlphaFold pLDDT 90.46

Full DYNLT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNLT3 p.Ala45Val Uncertain significance ★ ⚠ same type
DYNLT3 p.Ala75Thr Uncertain significance ★ ⚠ same type
DYNLT3 p.Arg101Trp Uncertain significance ★ same type
DYNLT3 p.Arg6Gly Uncertain significance ★ ⚠ same type
DYNLT3 p.Gln42Glu Uncertain significance ★ ⚠ same type
DYNLT3 p.His7Arg Uncertain significance ★ ⚠ same type
DYNLT3 p.Leu116Ile Uncertain significance ★ ⚠ same type
DYNLT3 p.Thr88Ile 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/dynlt3-p-ala61 (accessed [today's date]).

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