What condition is associated with LDHB p.Pro293= (c.879A>G)?

LDHB p.Pro293= (c.879A>G) is associated with glycogen storage disease due to lactate dehydrogenase H-subunit deficiency (ClinVar).

LDHB p.Pro293=

Q: Is LDHB p.Pro293= (c.879A>G) pathogenic?

LDHB p.Pro293= (c.879A>G) is classified Benign in LDHB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2018-09-19). Common (popmax 6.46%, afr) — too common for a highly-penetrant pathogenic allele; Associated with glycogen storage disease due to lactate dehydrogenase H-subunit deficiency.

Q: How common is LDHB p.Pro293= (c.879A>G) in the general population?

LDHB p.Pro293= (c.879A>G) is common (popmax 6.46%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.879A>G · rs4828 · VCV308015

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 6.46%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

glycogen storage disease due to lactate dehydrogenase H-subunit 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 -20	GERP -3.9
Overall
CADD	0.029	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.46% African / African-American · 4,846/74,974 alleles

Filtering AF 6.31% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.25%

Overall 0.34% 5,489/1,613,708 alleles · common exomes 2,735/1,461,552 · genomes 2,754/152,156 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.46%	15
Remaining individualsnot grpmax-eligible	0.504%	198
Admixed American	0.419%	239
Middle Eastern	0.182%	548
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,802
European (non-Finnish)	0.00509%	19,663
South Asian	0.00329%	30,358
Finnishnot grpmax-eligible	0.00156%	63,994

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: LDHB
Protein: p.Pro293=
Coding: c.879A>G
MANE Select: NM_002300
dbSNP: rs4828
Type: single nucleotide variant
Location: chr12:21635668 (GRCh38)
Gene constraint: LOEUF 0.927 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.05 · 7 PDB
Residue 293: a β-strand

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

Disease context

glycogen storage disease due to lactate dehydrogenase H-subunit deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycogen storage disease due to lactate dehydrogenase deficiency (Orphanet):

Onset: Childhood

Similar variants

LDHB p.Pro293Ala Uncertain significance ★ ⚠ same residue
LDHB p.Asn250Ser Uncertain significance ★★ ⚠ same condition
LDHB p.Ile261Thr Uncertain significance ★★ ⚠ same condition
LDHB p.Ser256Asn Uncertain significance ★★ ⚠ same condition
LDHB c.713+15A>G Benign ★★ same condition
LDHB c.129+11A>G Uncertain significance ★ same condition
LDHB c.130-8G>A Conflicting classifications of pathogenicity ★ same condition
LDHB c.421+7T>C 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/ldhb-p-pro293 (accessed [today's date]).

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