Is TECPR2 c.480+8del pathogenic?

TECPR2 c.480+8del is classified Likely benign in TECPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-25). No gnomAD frequency available for this variant; Associated with hereditary spastic paraplegia 49.

What condition is associated with TECPR2 c.480+8del?

TECPR2 c.480+8del is associated with hereditary spastic paraplegia 49 (ClinVar).

How common is TECPR2 c.480+8del in the general population?

TECPR2 c.480+8del is no gnomAD frequency available for this variant (gnomAD).

TECPR2 c.480+8del

Q: How is Hereditary sensory and autonomic neuropathy due to TECPR2 mutation inherited?

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

rs2504374524 · VCV2023970

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary spastic paraplegia 49

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +8	near-intronic (+8 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.5	GERP -1.9
Non-coding constraint	Z 1.72	1 kb window · o/e 0.87 · regional · uncalibrated

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: TECPR2
Coding: c.480+8del
MANE Select: NM_014844
dbSNP: rs2504374524
Type: Deletion
Location: chr14:102408626 (GRCh38)
Gene constraint: LOEUF 0.607 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.27

Full TECPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary spastic paraplegia 49 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary sensory and autonomic neuropathy due to TECPR2 mutation (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

TECPR2 c.222delG Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Asn1277fs Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Asn944fs Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Asp259fs Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Gln1263fs Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Gly584fs Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Leu1139fs Pathogenic ★★ same condition
TECPR2 p.Leu440fs 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/tecpr2-c-480-plus-8del (accessed [today's date]).

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