Is TANGO2 p.Phe119fs (c.357_358del) pathogenic?

TANGO2 p.Phe119fs (c.357358del) is classified Pathogenic in TANGO2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-24). No gnomAD frequency available for this variant.

How common is TANGO2 p.Phe119fs (c.357_358del) in the general population?

TANGO2 p.Phe119fs (c.357_358del) is no gnomAD frequency available for this variant (gnomAD).

TANGO2 p.Phe119fs

c.357_358del · rs2518826842 · VCV2710212

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TANGO2
Protein: p.Phe119fs
Coding: c.357_358del
MANE Select: NM_152906
dbSNP: rs2518826842
Type: Deletion
Location: chr22:20053528 (GRCh38)
Gene constraint: LOEUF 0.914 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.43 · 3 PDB
Residue 119: a UniProt-annotated variant site (in mecrcn); a β-strand

Full TANGO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TANGO2 p.Phe119= Likely benign ★ same residue
TANGO2 c.57-1743_*10769del Pathogenic ★★ same type
TANGO2 p.Cys2fs Pathogenic/Likely pathogenic ★★ same type
TANGO2 p.His94fs Pathogenic/Likely pathogenic ★★ same type
TANGO2 p.Pro12fs Pathogenic ★★ same type
TANGO2 c.146-3605_451+2245del Pathogenic ★ same type
TANGO2 p.Glu53fs Pathogenic ★ same type
TANGO2 p.Ile190_Leu197del Likely pathogenic ★ same type

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/tango2-p-phe119fs (accessed [today's date]).

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