Is TECPR2 p.Ser401= (c.1203C>T) pathogenic?

TECPR2 p.Ser401= (c.1203C>T) is classified Conflicting classifications of pathogenicity in TECPR2 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2023-10-27). Ultra-rare (popmax 0.0483%, sas); Associated with hereditary spastic paraplegia 49.

What condition is associated with TECPR2 p.Ser401= (c.1203C>T)?

TECPR2 p.Ser401= (c.1203C>T) is associated with hereditary spastic paraplegia 49, hereditary spastic paraplegia (ClinVar).

How common is TECPR2 p.Ser401= (c.1203C>T) in the general population?

TECPR2 p.Ser401= (c.1203C>T) is ultra-rare (popmax 0.0483%, sas) (gnomAD).

TECPR2 p.Ser401=

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.

c.1203C>T · rs759378757 · VCV989666

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0483%, sas)

Conditions

hereditary spastic paraplegia 49

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 -20	GERP -3
Overall
CADD	0.439	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0483% South Asian · 44/91,016 alleles

Filtering AF 0.0369% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.033%

Overall 0.00677% 109/1,610,820 alleles · ultra-rare exomes 104/1,458,628 · genomes 5/152,192 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0483%	2,069
Middle Eastern	0.0329%	3,038
African / African-American	0.00668%	14,979
Remaining individualsnot grpmax-eligible	0.00642%	15,571
European (non-Finnish)	0.0045%	22,223
Finnishnot grpmax-eligible	0.00158%	63,448

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: TECPR2
Protein: p.Ser401=
Coding: c.1203C>T
MANE Select: NM_014844
dbSNP: rs759378757
Type: single nucleotide variant
Location: chr14:102431914 (GRCh38)
Gene constraint: LOEUF 0.607 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.27
Residue 401: the 'disordered' region

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

Also linked: hereditary spastic paraplegia

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

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

TECPR2 c.1084+2T>C Likely pathogenic ★★ same condition
TECPR2 c.1418-2A>G Likely pathogenic ★★ same condition
TECPR2 c.2753-1G>A Likely pathogenic ★★ same condition
TECPR2 p.Gln1189Ter Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Gln191Ter Pathogenic/Likely pathogenic ★★ same condition
TECPR2 p.Gln852Ter Pathogenic ★★ same condition
TECPR2 p.Trp1024Ter Pathogenic ★★ same condition
TECPR2 p.Trp1288Ter 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-p-ser401 (accessed [today's date]).

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