Is TPP2 p.Tyr1069= (c.3207C>T) pathogenic?

TPP2 p.Tyr1069= (c.3207C>T) is classified Likely benign in TPP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-23). Very rare (popmax 0.00342%, amr); Associated with Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency.

How common is TPP2 p.Tyr1069= (c.3207C>T) in the general population?

TPP2 p.Tyr1069= (c.3207C>T) is very rare (popmax 0.00342%, amr) (gnomAD).

TPP2 p.Tyr1069=

Q: What condition is associated with TPP2 p.Tyr1069= (c.3207C>T)?

TPP2 p.Tyr1069= (c.3207C>T) is associated with Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency (ClinVar).

c.3207C>T · rs768789175 · VCV1118105

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00342%, amr)

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	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -7.3	GERP -4.7
Overall
CADD	0.628	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00342% Admixed American · 2/58,554 alleles

Filtering AF 0.000567% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000367%

Overall 0.000997% 16/1,605,486 alleles · very rare exomes 15/1,453,350 · genomes 1/152,136 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00342%	29,277
East Asian	0.00225%	44,398
Remaining individualsnot grpmax-eligible	0.00161%	62,166
South Asian	0.00113%	88,768
European (non-Finnish)	0.000934%	107,016

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.Tyr1069=
Coding: c.3207C>T
MANE Select: NM_001330588
dbSNP: rs768789175
Type: single nucleotide variant
Location: chr13:102663711 (GRCh38)
Gene constraint: LOEUF 0.29 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 91.98
Residue 1069: a UniProt-annotated variant site (in imd78; loss of expression)

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-tyr1069 (accessed [today's date]).

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