Is TPP2 p.Ser679= (c.2037G>A) pathogenic?

TPP2 p.Ser679= (c.2037G>A) is classified Likely benign in TPP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-29). Very rare (popmax 0.00906%, sas); Associated with Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency.

How common is TPP2 p.Ser679= (c.2037G>A) in the general population?

TPP2 p.Ser679= (c.2037G>A) is very rare (popmax 0.00906%, sas) (gnomAD).

TPP2 p.Ser679=

Q: What condition is associated with TPP2 p.Ser679= (c.2037G>A)?

TPP2 p.Ser679= (c.2037G>A) is associated with Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency (ClinVar).

c.2037G>A · rs149060291 · VCV1099846

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00906%, sas)

Conditions

Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.52 · evaluated, not missing
Constraint at this position
Conservation	phyloP -6.2	GERP -5
Overall
CADD	0.967	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00906% South Asian · 8/88,296 alleles

Filtering AF 0.00449% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00321%

Overall 0.00162% 26/1,601,844 alleles · very rare exomes 24/1,449,722 · genomes 2/152,122 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00906%	11,037
Remaining individualsnot grpmax-eligible	0.00161%	61,950
European (non-Finnish)	0.00145%	69,189

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: TPP2
Protein: p.Ser679=
Coding: c.2037G>A
MANE Select: NM_001330588
dbSNP: rs149060291
Type: single nucleotide variant
Location: chr13:102643238 (GRCh38)
Gene constraint: LOEUF 0.29 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 91.98

Full TPP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TPP2 p.Ala619Thr Uncertain significance ★★ ⚠ same condition
TPP2 p.Ala648Asp Uncertain significance ★★ ⚠ same condition
TPP2 p.Arg1072Gln Uncertain significance ★★ ⚠ same condition
TPP2 p.Arg893Cys Uncertain significance ★★ ⚠ same condition
TPP2 p.Asn1192Ser Uncertain significance ★★ ⚠ same condition
TPP2 p.Asn1227Ser Uncertain significance ★★ ⚠ same condition
TPP2 p.Asp86His Uncertain significance ★★ ⚠ same condition
TPP2 p.Cys1231Tyr 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/tpp2-p-ser679 (accessed [today's date]).

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