Is CSTB p.Ala49= (c.147G>A) pathogenic?

CSTB p.Ala49= (c.147G>A) is classified Likely benign in CSTB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-24). Very rare (popmax 0.00695%, nfe); Associated with progressive myoclonus epilepsy.

What condition is associated with CSTB p.Ala49= (c.147G>A)?

CSTB p.Ala49= (c.147G>A) is associated with progressive myoclonus epilepsy (ClinVar).

How common is CSTB p.Ala49= (c.147G>A) in the general population?

CSTB p.Ala49= (c.147G>A) is very rare (popmax 0.00695%, nfe) (gnomAD).

CSTB p.Ala49=

c.147G>A · rs766654703 · VCV1095605

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00695%, nfe)

Conditions

progressive myoclonus epilepsy

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 -4.2
Overall
CADD	0.327	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00695% European (non-Finnish) · 82/1,179,972 alleles

Filtering AF 0.00571% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00525%

Overall 0.00551% 89/1,613,984 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00695%	14,390
Remaining individualsnot grpmax-eligible	0.0048%	20,829
East Asian	0.00446%	22,445
Admixed American	0.00333%	30,004

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.Ala49=
Coding: c.147G>A
MANE Select: NM_000100
dbSNP: rs766654703
Type: single nucleotide variant
Location: chr21:43774679 (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 49: 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.Ala49Thr Uncertain significance ★★ ⚠ same residue
CSTB p.Ala49Glu Uncertain significance ★ ⚠ same residue
CSTB p.Ala49fs Pathogenic ★★ same residue
CSTB p.Ala49Val Uncertain significance ★ ⚠ 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

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-ala49 (accessed [today's date]).

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