What condition is associated with LDHA p.Ser161= (c.483C>T)?

LDHA p.Ser161= (c.483C>T) is associated with glycogen storage disease due to lactate dehydrogenase M-subunit deficiency (ClinVar).

LDHA p.Ser161=

Q: Is LDHA p.Ser161= (c.483C>T) pathogenic?

LDHA p.Ser161= (c.483C>T) is classified Benign in LDHA (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). Common (popmax 74.8%, sas) — too common for a highly-penetrant pathogenic allele; Associated with glycogen storage disease due to lactate dehydrogenase M-subunit deficiency.

Q: How common is LDHA p.Ser161= (c.483C>T) in the general population?

LDHA p.Ser161= (c.483C>T) is common (popmax 74.8%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.483C>T · rs4687 · VCV303914

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 74.8%, sas) — too common for a highly-penetrant pathogenic allele

Conditions

glycogen storage disease due to lactate dehydrogenase M-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 1.5	GERP 0.79, phastCons 1
Overall
CADD	11.05	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 74.8% South Asian · 68,051/90,932 alleles

Filtering AF 74.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 74.2%

Overall 70.9% 1,139,453/1,607,204 alleles · common

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	79%	1
South Asiangrpmax	74.8%	1
Amishnot grpmax-eligible	73.4%	1
European (non-Finnish)	72.1%	1
Admixed American	72%	1
Middle Eastern	71.3%	1
Remaining individualsnot grpmax-eligible	69.9%	1
East Asian	66%	2
Ashkenazi Jewishnot grpmax-eligible	60.8%	2
African / African-American	47.1%	2

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: LDHA
Protein: p.Ser161=
Coding: c.483C>T
MANE Select: NM_005566
dbSNP: rs4687
Type: single nucleotide variant
Location: chr11:18402904 (GRCh38)
Gene constraint: LOEUF 0.613 · pLI 0.77 (gnomAD)
Structure: AlphaFold pLDDT 96.08 · 46 PDB

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

Disease context

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

Similar variants

LDHA p.Ser137Ter Pathogenic ★★ same condition
LDHA c.*660C>T Uncertain significance ★★ same condition
LDHA p.Arg112Cys Uncertain significance ★★ ⚠ same condition
LDHA p.Arg157His Uncertain significance ★★ ⚠ same condition
LDHA p.Asp285Val Uncertain significance ★★ ⚠ same condition
LDHA p.Asp46Val Uncertain significance ★★ ⚠ same condition
LDHA p.Ile159Asn Uncertain significance ★★ ⚠ same condition
LDHA p.Lys149Glu 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/ldha-p-ser161 (accessed [today's date]).

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