Is TONSL p.Ala832= (c.2496C>T) pathogenic?

TONSL p.Ala832= (c.2496C>T) is classified Benign in TONSL (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-04). Common (popmax 57.8%, sas) — too common for a highly-penetrant pathogenic allele; Associated with spondyloepimetaphyseal dysplasia, sponastrime type.

What condition is associated with TONSL p.Ala832= (c.2496C>T)?

TONSL p.Ala832= (c.2496C>T) is associated with spondyloepimetaphyseal dysplasia, sponastrime type (ClinVar).

How is SPONASTRIME dysplasia inherited?

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

TONSL p.Ala832=

Q: How common is TONSL p.Ala832= (c.2496C>T) in the general population?

TONSL p.Ala832= (c.2496C>T) is common (popmax 57.8%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2496C>T · rs2721140 · VCV1167020

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 57.8%, sas) — too common for a highly-penetrant pathogenic allele

Conditions

spondyloepimetaphyseal dysplasia, sponastrime type

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 -3	GERP -3
Overall
CADD	0.224	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 57.8% South Asian · 49,872/86,214 alleles

Filtering AF 57.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 57.2%

Overall 46.8% 732,512/1,565,840 alleles · common exomes 664,378/1,413,824 · genomes 68,134/152,016 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	57.8%	2
Amishnot grpmax-eligible	51.5%	2
Finnishnot grpmax-eligible	48%	2
European (non-Finnish)	47.3%	2
Remaining individualsnot grpmax-eligible	45.5%	2
Admixed American	42.3%	2
African / African-American	41.7%	2
East Asian	37.1%	3
Middle Eastern	36.5%	3
Ashkenazi Jewishnot grpmax-eligible	32%	3

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: TONSL
Protein: p.Ala832=
Coding: c.2496C>T
MANE Select: NM_013432
dbSNP: rs2721140
Type: single nucleotide variant
Location: chr8:144435937 (GRCh38)
Gene constraint: LOEUF 1.024 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.06 · 3 PDB
Residue 832: a UniProt-annotated variant site (in semdsp; disease phenotype includes immunologic and hematologic abnormalities); a UniProt-annotated variant site (in semdsp); a UniProt-annotated variant site (in semdsp; disease phenotype includes primary aphakia and absent pupils)

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

Disease context

spondyloepimetaphyseal dysplasia, sponastrime type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For SPONASTRIME dysplasia (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

TONSL c.1891-1G>C Pathogenic/Likely pathogenic ★★ same condition
TONSL p.Arg875Ter Pathogenic/Likely pathogenic ★★ same condition
TONSL p.Arg934Trp Pathogenic ★★ ⚠ same condition
TONSL p.Gln511Ter Pathogenic/Likely pathogenic ★★ same condition
TONSL p.Glu487Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
TONSL p.Ala1092Val Uncertain significance ★★ ⚠ same condition
TONSL p.Ala192Val Uncertain significance ★★ ⚠ same condition
TONSL p.Ala964Val 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/tonsl-p-ala832 (accessed [today's date]).

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