Is PRDM8 p.Pro656= (c.1968C>G) pathogenic?

PRDM8 p.Pro656= (c.1968C>G) is classified Likely benign in PRDM8 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-15). Ultra-rare (popmax 0.0341%, sas); Associated with early-onset Lafora body disease.

What condition is associated with PRDM8 p.Pro656= (c.1968C>G)?

PRDM8 p.Pro656= (c.1968C>G) is associated with early-onset Lafora body disease (ClinVar).

How common is PRDM8 p.Pro656= (c.1968C>G) in the general population?

PRDM8 p.Pro656= (c.1968C>G) is ultra-rare (popmax 0.0341%, sas) (gnomAD).

How is PRDM8-related progressive myoclonus epilepsy inherited?

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

PRDM8 p.Pro656=

c.1968C>G · rs547453696 · VCV475678

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0341%, sas)

Conditions

early-onset Lafora body disease

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 0.45	GERP -1.3, phastCons 0.047
Overall
CADD	10.19	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0341% South Asian · 31/90,896 alleles

Filtering AF 0.0247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0214%

Overall 0.0026% 42/1,613,506 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0341%	2,932
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.008%	12,493
European (non-Finnish)	0.000424%	235,973

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: PRDM8
Protein: p.Pro656=
Coding: c.1968C>G
MANE Select: NM_001099403
dbSNP: rs547453696
Type: single nucleotide variant
Location: chr4:80203430 (GRCh38)
Gene constraint: LOEUF 0.498 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 55.64

Full PRDM8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

early-onset Lafora body disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For PRDM8-related progressive myoclonus epilepsy (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

PRDM8 p.Pro656Ser Uncertain significance ★★ ⚠ same residue
PRDM8 p.Pro656Leu Uncertain significance ★ ⚠ same residue
PRDM8 p.Ala372Thr Uncertain significance ★★ ⚠ same condition
PRDM8 p.Ala416Thr Uncertain significance ★★ ⚠ same condition
PRDM8 p.Ala529Val Uncertain significance ★★ ⚠ same condition
PRDM8 p.Ala540Ser Uncertain significance ★★ ⚠ same condition
PRDM8 p.Ala541Ser Uncertain significance ★★ ⚠ same condition
PRDM8 p.Ala546Val 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/prdm8-p-pro656 (accessed [today's date]).

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