Is TECPR2 p.Ser236= (c.708A>G) pathogenic?

TECPR2 p.Ser236= (c.708A>G) is classified Conflicting classifications of pathogenicity in TECPR2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-08-01). Absent from gnomAD v4.1; Associated with hereditary spastic paraplegia.

What condition is associated with TECPR2 p.Ser236= (c.708A>G)?

TECPR2 p.Ser236= (c.708A>G) is associated with hereditary spastic paraplegia (ClinVar).

How common is TECPR2 p.Ser236= (c.708A>G) in the general population?

TECPR2 p.Ser236= (c.708A>G) is absent from gnomAD v4.1 (gnomAD).

TECPR2 p.Ser236=

c.708A>G · rs2139716000 · VCV1344162

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary spastic paraplegia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -6.4	GERP -3.2
Overall
CADD	0.432	PHRED · no single calibrated threshold — expert panels disagree

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: TECPR2
Protein: p.Ser236=
Coding: c.708A>G
MANE Select: NM_014844
dbSNP: rs2139716000
Type: single nucleotide variant
Location: chr14:102425048 (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 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TECPR2 p.Ala1156Thr Uncertain significance ★★ ⚠ same condition
TECPR2 p.Arg1159Trp Uncertain significance ★★ ⚠ same condition
TECPR2 p.Arg273His Uncertain significance ★★ ⚠ same condition
TECPR2 p.Arg943Trp Uncertain significance ★★ ⚠ same condition
TECPR2 p.Arg959Trp Uncertain significance ★★ ⚠ same condition
TECPR2 p.Gly1266Val Uncertain significance ★★ ⚠ same condition
TECPR2 p.Gly536Ser Uncertain significance ★★ ⚠ same condition
TECPR2 p.Ser1129Tyr Uncertain significance ★★ ⚠ 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-p-ser236 (accessed [today's date]).

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