Is DLD p.Asn93Ser (c.278A>G) pathogenic?

DLD p.Asn93Ser (c.278A>G) is classified Uncertain significance in DLD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-20). AlphaMissense: likely benign (0.1818); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DLD p.Asn93Ser (c.278A>G)?

DLD p.Asn93Ser (c.278A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DLD p.Asn93Ser (c.278A>G) in the general population?

DLD p.Asn93Ser (c.278A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DLD p.Asn93Ser (c.278A>G)?

AlphaMissense predicts likely benign (score 0.1818) — an in-silico prediction, not a clinical call.

DLD p.Asn93Ser

c.278A>G · VCV3840264

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1818 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,584,732)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1818	likely benign
REVEL	0.357	indeterminate
SaProt	LLR -10.16	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 28 kb · p 0.0061 · regional, not allelic
Overall
CADD	26.3	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

No allele count reported in gnomAD v4.1 (AN 1,584,732). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DLD
Protein: p.Asn93Ser
Coding: c.278A>G
MANE Select: NM_000108
Type: single nucleotide variant
Location: chr7:107903488 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.69 · 17 PDB
Residue 93: an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DLD p.Ala501Val Uncertain significance ★★ ⚠ same condition
DLD p.Gly154Glu Uncertain significance ★★ ⚠ same condition
DLD p.Gly287Glu Uncertain significance ★★ same condition
DLD p.Lys410Gln Uncertain significance ★★ ⚠ same condition
DLD p.Met255Thr Uncertain significance ★★ ⚠ same condition
DLD p.Thr157Ser Uncertain significance ★★ ⚠ same condition
DLD p.Thr171Pro Uncertain significance ★★ ⚠ same condition
DLD p.Tyr386Cys 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/dld-p-asn93ser (accessed [today's date]).

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