Is TK2 p.Pro31fs (c.87del) pathogenic?

TK2 p.Pro31fs (c.87del) is classified Pathogenic in TK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-27). No allele count reported in gnomAD v4.1 (AN 1,487,604).

How common is TK2 p.Pro31fs (c.87del) in the general population?

TK2 p.Pro31fs (c.87del) is no allele count reported in gnomAD v4.1 (AN 1,487,604) (gnomAD).

TK2 p.Pro31fs

c.87del · rs1163069592 · VCV951349

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,487,604)

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 1 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.3	GERP -2.6

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,487,604). 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: TK2
Protein: p.Pro31fs
Coding: c.87del
MANE Select: NM_004614
dbSNP: rs1163069592
Type: Deletion
Location: chr16:66549975 (GRCh38)
Gene constraint: LOEUF 1.101 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.01
Residue 31: the 'disordered' region

Full TK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TK2 c.125-1_127del Pathogenic/Likely pathogenic ★★ same type
TK2 c.536_538+8del Pathogenic/Likely pathogenic ★★ same type
TK2 p.Ala230fs Pathogenic/Likely pathogenic ★★ same type
TK2 p.Leu182fs Pathogenic/Likely pathogenic ★★ same type
TK2 p.Lys202del Pathogenic/Likely pathogenic ★★ same type
TK2 p.Lys43fs Pathogenic ★★ same type
TK2 p.Tyr148fs Pathogenic/Likely pathogenic ★★ same type
TK2 p.Asp119fs 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/tk2-p-pro31fs (accessed [today's date]).

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