Is BSCL2 p.Ser154Ala (c.460T>G) pathogenic?

BSCL2 p.Ser154Ala (c.460T>G) is classified Conflicting classifications of pathogenicity in BSCL2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-10-22). AlphaMissense: likely benign (0.1701); Absent from gnomAD v4.1; Associated with hereditary spastic paraplegia 17.

What condition is associated with BSCL2 p.Ser154Ala (c.460T>G)?

BSCL2 p.Ser154Ala (c.460T>G) is associated with hereditary spastic paraplegia 17, Charcot-Marie-Tooth disease type 2, neuronopathy, distal hereditary motor, type 5C (ClinVar).

How common is BSCL2 p.Ser154Ala (c.460T>G) in the general population?

BSCL2 p.Ser154Ala (c.460T>G) is absent from gnomAD v4.1 (gnomAD).

How is Autosomal dominant spastic paraplegia type 17 inherited?

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

What do computational predictors say about BSCL2 p.Ser154Ala (c.460T>G)?

AlphaMissense predicts likely benign (score 0.1701) — an in-silico prediction, not a clinical call.

BSCL2 p.Ser154Ala

c.460T>G · rs1590881633 · VCV643607

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1701 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary spastic paraplegia 17

Computational evidence

Protein change
AlphaMissense	0.1701	likely benign
REVEL	0.674	pathogenic-leaning
SaProt	LLR -11.59	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 1.3, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 13 kb · p 0.65 · regional, not allelic
Overall
CADD	22.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S90A vs ClinVar S154A) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BSCL2
Protein: p.Ser154Ala
Coding: c.460T>G
MANE Select: NM_001122955
dbSNP: rs1590881633
Type: single nucleotide variant
Location: chr11:62702494 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.09 · 1 PDB
Residue 154: the 'hydrophobic helix' region

Full BSCL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary spastic paraplegia 17 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Charcot-Marie-Tooth disease type 2 neuronopathy, distal hereditary motor, type 5C

For Autosomal dominant spastic paraplegia type 17 (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

BSCL2 p.Ser154Leu Pathogenic/Likely pathogenic ★★ ⚠ same residue
BSCL2 p.Ser154Trp Pathogenic ★★ same residue
BSCL2 p.Ser154= Likely benign ★ same residue
BSCL2 c.1006-2A>C Likely pathogenic ★★ same condition
BSCL2 c.486+1G>A Pathogenic/Likely pathogenic ★★ same condition
BSCL2 p.Ala276Pro Pathogenic ★★ same condition
BSCL2 p.Arg202Ter Pathogenic ★★ same condition
BSCL2 p.Arg329Ter 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/bscl2-p-ser154ala (accessed [today's date]).

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