Is TECPR2 p.Ser559= (c.1677T>C) pathogenic?

TECPR2 p.Ser559= (c.1677T>C) is classified Likely benign in TECPR2 (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-28). Ultra-rare (popmax 0.0789%, afr); Associated with hereditary spastic paraplegia 49.

What condition is associated with TECPR2 p.Ser559= (c.1677T>C)?

TECPR2 p.Ser559= (c.1677T>C) is associated with hereditary spastic paraplegia 49 (ClinVar).

How common is TECPR2 p.Ser559= (c.1677T>C) in the general population?

TECPR2 p.Ser559= (c.1677T>C) is ultra-rare (popmax 0.0789%, afr) (gnomAD).

TECPR2 p.Ser559=

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.1677T>C · rs375017422 · VCV1124190

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0789%, afr)

Conditions

hereditary spastic paraplegia 49

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.3	GERP -3.2
Overall
CADD	0.021	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0789% African / African-American · 58/73,550 alleles

Filtering AF 0.0625% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0567%

Overall 0.00454% 71/1,562,176 alleles · ultra-rare exomes 34/1,409,872 · genomes 37/152,304 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0789%	1,268
South Asian	0.00849%	11,777
East Asian	0.00675%	14,824
Admixed American	0.00381%	26,275
Remaining individualsnot grpmax-eligible	0.00166%	60,260

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.Ser559=
Coding: c.1677T>C
MANE Select: NM_014844
dbSNP: rs375017422
Type: single nucleotide variant
Location: chr14:102434494 (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.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-ser559 (accessed [today's date]).

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