Is SETX p.Val715fs (c.2143_2144del) pathogenic?

SETX p.Val715fs (c.21432144del) is classified Likely pathogenic in SETX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-21). No gnomAD frequency available for this variant.

How common is SETX p.Val715fs (c.2143_2144del) in the general population?

SETX p.Val715fs (c.2143_2144del) is no gnomAD frequency available for this variant (gnomAD).

SETX p.Val715fs

c.2143_2144del · rs2539125316 · VCV2433320

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 10 of 26
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1	GERP -3.6

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: SETX
Protein: p.Val715fs
Coding: c.2143_2144del
MANE Select: NM_015046
dbSNP: rs2539125316
Type: Deletion
Location: chr9:132329454 (GRCh38)
Gene constraint: LOEUF 0.442 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 52.93

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

Similar variants

SETX c.6843-3_6843-1del Likely pathogenic ★★ same type
SETX c.6848_6851del Pathogenic ★★ same type
SETX p.Asp2332fs Pathogenic/Likely pathogenic ★★ same type
SETX p.Gln1864fs Pathogenic/Likely pathogenic ★★ same type
SETX p.Lys796fs Pathogenic ★★ same type
SETX p.Thr1755fs Pathogenic ★★ same type
SETX p.Arg2529fs Uncertain significance ★★ same type
SETX p.His476_Leu477del Uncertain significance ★★ same type

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/setx-p-val715fs (accessed [today's date]).

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