Is SACS p.Leu796fs (c.2387del) pathogenic?

SACS p.Leu796fs (c.2387del) is classified Pathogenic in SACS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). Absent from gnomAD; Associated with Charlevoix-Saguenay spastic ataxia.

What condition is associated with SACS p.Leu796fs (c.2387del)?

SACS p.Leu796fs (c.2387del) is associated with Charlevoix-Saguenay spastic ataxia (ClinVar).

How common is SACS p.Leu796fs (c.2387del) in the general population?

SACS p.Leu796fs (c.2387del) is absent from gnomAD (gnomAD).

SACS p.Leu796fs

Q: How is Autosomal recessive spastic ataxia of Charlevoix-Saguenay inherited?

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

c.2387del · rs2542314342 · VCV2572089

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Charlevoix-Saguenay spastic ataxia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (10 of 10) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.024	GERP -0.34, phastCons 0.91

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SACS
Protein: p.Leu796fs
Coding: c.2387del
MANE Select: NM_014363
dbSNP: rs2542314342
Type: Deletion
Location: chr13:23341489 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

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

Disease context

Charlevoix-Saguenay spastic ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal recessive spastic ataxia of Charlevoix-Saguenay (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy

Similar variants

SACS p.Ala1723fs Pathogenic/Likely pathogenic ★★ same condition
SACS p.Ala2208fs Pathogenic/Likely pathogenic ★★ same condition
SACS p.Arg624fs Pathogenic/Likely pathogenic ★★ same condition
SACS p.Arg919fs Pathogenic/Likely pathogenic ★★ same condition
SACS p.Asn1025fs Pathogenic/Likely pathogenic ★★ same condition
SACS p.Asn1586fs Pathogenic ★★ same condition
SACS p.Asn1616fs Likely pathogenic ★★ same condition
SACS p.Asn2380fs 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/sacs-p-leu796fs (accessed [today's date]).

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