Is DLD c.*855C>T pathogenic?

DLD c.855C>T is classified Benign in DLD (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Low-frequency (popmax 4.74%, afr); Associated with pyruvate dehydrogenase E3 deficiency.

What condition is associated with DLD c.*855C>T?

DLD c.*855C>T is associated with pyruvate dehydrogenase E3 deficiency, Leigh syndrome, pyruvate dehydrogenase deficiency (ClinVar).

How common is DLD c.*855C>T in the general population?

DLD c.*855C>T is low-frequency (popmax 4.74%, afr) (gnomAD).

How is Maple syrup urine disease inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DLD c.*855C>T

rs116055514 · VCV358582

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 4.74%, afr)

Conditions

pyruvate dehydrogenase E3 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -1.9
Overall
CADD	4.172	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.74% African / African-American · 1,965/41,468 alleles

Filtering AF 4.56% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.49%

Overall 1.36% 2,063/152,106 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.74%	21
Remaining individualsnot grpmax-eligible	0.994%	101
Admixed American	0.431%	232
South Asian	0.0207%	4,824
European (non-Finnish)	0.0147%	6,798

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: DLD
Coding: c.*855C>T
MANE Select: NM_000108
dbSNP: rs116055514
Type: single nucleotide variant
Location: chr7:107920114 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.69 · 17 PDB

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

Disease context

pyruvate dehydrogenase E3 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Leigh syndrome pyruvate dehydrogenase deficiency

For Maple syrup urine disease (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

DLD c.1464+1G>A Pathogenic/Likely pathogenic ★★ same condition
DLD c.198+1G>T Likely pathogenic ★★ same condition
DLD c.39+1G>A Likely pathogenic ★★ same condition
DLD c.40-2A>G Likely pathogenic ★★ same condition
DLD c.583-1G>C Likely pathogenic ★★ same condition
DLD c.684+1G>T Likely pathogenic ★★ same condition
DLD c.875+1G>A Pathogenic/Likely pathogenic ★★ same condition
DLD p.Arg315Ter Likely pathogenic ★★ 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-c-star-855c-t (accessed [today's date]).

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