Is CSTB p.Lys56Arg (c.167A>G) pathogenic?

CSTB p.Lys56Arg (c.167A>G) is classified Uncertain significance in CSTB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-08-10). AlphaMissense: likely benign (0.1588); Very rare (popmax 0.00534%, afr); Associated with progressive myoclonus epilepsy.

What condition is associated with CSTB p.Lys56Arg (c.167A>G)?

CSTB p.Lys56Arg (c.167A>G) is associated with progressive myoclonus epilepsy (ClinVar).

How common is CSTB p.Lys56Arg (c.167A>G) in the general population?

CSTB p.Lys56Arg (c.167A>G) is very rare (popmax 0.00534%, afr) (gnomAD).

What do computational predictors say about CSTB p.Lys56Arg (c.167A>G)?

AlphaMissense predicts likely benign (score 0.1588) — an in-silico prediction, not a clinical call.

CSTB p.Lys56Arg

c.167A>G · rs935774172 · VCV373528

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1588 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

progressive myoclonus epilepsy

Computational evidence

Protein change
AlphaMissense	0.1588	likely benign
REVEL	0.197	benign-leaning
SaProt	LLR -11.44	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	Δ0.43	donor gain · deltas
Pangolin	Δ0.31	loss · gain 0.28 · SpliceAI calls gain · independent
Constraint at this position
Conservation	phyloP 7.3	GERP 1.1, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 2,064 bp · p 0.83 · regional, not allelic
Overall
CADD	26.7	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

Grpmax group 0.00534% African / African-American · 4/74,914 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000372% 6/1,612,978 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00534%	18,728
Admixed American	0.00167%	59,998
European (non-Finnish)	8.48e-05%	1,179,076

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: CSTB
Protein: p.Lys56Arg
Coding: c.167A>G
MANE Select: NM_000100
dbSNP: rs935774172
Type: single nucleotide variant
Location: chr21:43774659 (GRCh38)
Gene constraint: LOEUF 1.681 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 95.81 · 3 PDB
Residue 56: a β-strand

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

Disease context

progressive myoclonus epilepsy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CSTB p.Lys56= Likely pathogenic same residue
CSTB c.67-1G>C Pathogenic ★★ same condition
CSTB p.Arg68Ter Pathogenic ★★ same condition
CSTB p.Gln22Ter Pathogenic/Likely pathogenic ★★ same condition
CSTB p.Gln46Ter Pathogenic/Likely pathogenic ★★ same condition
CSTB p.Ala49Thr Uncertain significance ★★ ⚠ same condition
CSTB p.Ala90Thr Uncertain significance ★★ ⚠ same condition
CSTB p.Asn52Ile 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/cstb-p-lys56arg (accessed [today's date]).

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