Is TERT p.Phe809fs (c.2426_2427del) pathogenic?

TERT p.Phe809fs (c.24262427del) is classified Likely pathogenic in TERT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-19). Absent from gnomAD; Associated with pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1.

What condition is associated with TERT p.Phe809fs (c.2426_2427del)?

TERT p.Phe809fs (c.2426_2427del) is associated with pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 (ClinVar).

How common is TERT p.Phe809fs (c.2426_2427del) in the general population?

TERT p.Phe809fs (c.2426_2427del) is absent from gnomAD (gnomAD).

TERT p.Phe809fs

c.2426_2427del · rs1749003568 · VCV1686799

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1

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 8 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.2	GERP 1.1, 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: TERT
Protein: p.Phe809fs
Coding: c.2426_2427del
MANE Select: NM_198253
dbSNP: rs1749003568
Type: Deletion
Location: chr5:1271160 (GRCh38)
Gene constraint: LOEUF 0.593 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 80.98 · 32 PDB
Residue 809: the reverse transcriptase domain; an α-helix

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

Disease context

pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TERT p.Cys998fs Pathogenic/Likely pathogenic ★★ same condition
TERT p.Asp685del Pathogenic ★ same condition
TERT p.Val461_Tyr462insTer Pathogenic ★ same condition
TERT p.Val747fs Pathogenic ★ same condition
TERT p.Phe809Tyr Uncertain significance ★ ⚠ same residue
TERT p.Phe809= Likely benign ★ same residue
TERT c.2131-2A>G Likely pathogenic ★★ same condition
TERT p.Ala1009Val Likely pathogenic ★★ 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/tert-p-phe809fs (accessed [today's date]).

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