Is TSFM p.Phe310fs (c.929_930del) pathogenic?

TSFM p.Phe310fs (c.929930del) is classified Pathogenic in TSFM (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-25). No gnomAD frequency available for this variant.

How common is TSFM p.Phe310fs (c.929_930del) in the general population?

TSFM p.Phe310fs (c.929_930del) is no gnomAD frequency available for this variant (gnomAD).

TSFM p.Phe310fs

c.929_930del · rs2540966023 · VCV2097083

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	escapes	premature termination codon in the last exon (6 of 6) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.23	GERP -2.2, phastCons 0.98

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: TSFM
Protein: p.Phe310fs
Coding: c.929_930del
MANE Select: NM_005726
dbSNP: rs2540966023
Type: Deletion
Location: chr12:57796533 (GRCh38)
Gene constraint: LOEUF 1.197 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.87 · 1 PDB
Residue 310: a UniProt-annotated variant site (in coxpd3)

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

Similar variants

TSFM p.Phe310= Likely benign ★ same residue
TSFM p.Asp184fs Pathogenic/Likely pathogenic ★★ same type
TSFM p.Leu137fs Pathogenic/Likely pathogenic ★★ same type
TSFM p.Lys133fs Pathogenic/Likely pathogenic ★★ same type
TSFM p.Met1fs Likely pathogenic ★★ same type
TSFM p.Arg25fs Likely pathogenic ★ same type
TSFM p.Arg312fs Likely pathogenic ★ same type
TSFM p.Gln139fs 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/tsfm-p-phe310fs (accessed [today's date]).

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