Is DYNC2LI1 p.Asp276= (c.828C>T) pathogenic?

DYNC2LI1 p.Asp276= (c.828C>T) is classified Likely benign in DYNC2LI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-18). Very rare (popmax 0.00343%, amr).

How common is DYNC2LI1 p.Asp276= (c.828C>T) in the general population?

DYNC2LI1 p.Asp276= (c.828C>T) is very rare (popmax 0.00343%, amr) (gnomAD).

DYNC2LI1 p.Asp276=

c.828C>T · VCV4703870

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00343%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.005	strongly benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.76	GERP -0.33, phastCons 1
Overall
CADD	7.694	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00343% Admixed American · 2/58,312 alleles

Filtering AF 0.000569% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000213%

Overall 0.000311% 5/1,605,996 alleles · very rare exomes 4/1,453,898 · genomes 1/152,098 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00343%	29,156
Remaining individualsnot grpmax-eligible	0.00161%	62,162
African / African-American	0.00134%	74,452
European (non-Finnish)	8.5e-05%	1,177,138

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: DYNC2LI1
Protein: p.Asp276=
Coding: c.828C>T
MANE Select: NM_016008
Type: single nucleotide variant
Location: chr2:43804667 (GRCh38)
Gene constraint: LOEUF 1.028 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.49 · 3 PDB

Full DYNC2LI1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNC2LI1 p.Asp276Asn Uncertain significance ★ ⚠ same residue
DYNC2LI1 p.Asp276Gly Uncertain significance ★ ⚠ same residue
DYNC2LI1 p.Leu117Val Pathogenic/Likely pathogenic ★★ ⚠ same type
DYNC2LI1 p.Trp124Ter Pathogenic/Likely pathogenic ★★ same type
ABCG5 p.Ala505Asp Uncertain significance ★★ ⚠ same type
ABCG5 p.Gly288Ser Uncertain significance ★★ ⚠ same type
ABCG5 p.Ser361Cys Uncertain significance ★★ ⚠ same type
ABCG5 p.Val420Gly 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/dync2li1-p-asp276 (accessed [today's date]).

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