Is TKFC p.Asp43fs (c.129_130del) pathogenic?

TKFC p.Asp43fs (c.129130del) is classified Uncertain significance in TKFC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-29). No gnomAD frequency available for this variant; Associated with triokinase and FMN cyclase deficiency syndrome.

What condition is associated with TKFC p.Asp43fs (c.129_130del)?

TKFC p.Asp43fs (c.129_130del) is associated with triokinase and FMN cyclase deficiency syndrome (ClinVar).

How common is TKFC p.Asp43fs (c.129_130del) in the general population?

TKFC p.Asp43fs (c.129_130del) is no gnomAD frequency available for this variant (gnomAD).

TKFC p.Asp43fs

c.129_130del · rs2539727234 · VCV3065703

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

triokinase and FMN cyclase deficiency syndrome

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 3 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 10	GERP 2.3, 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: TKFC
Protein: p.Asp43fs
Coding: c.129_130del
MANE Select: NM_015533
dbSNP: rs2539727234
Type: Deletion
Location: chr11:61338065 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.40
Residue 43: the dhak domain

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

Disease context

triokinase and FMN cyclase deficiency syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TKFC p.Arg543Ile Likely pathogenic ★★ same condition
TKFC p.Arg228Gln Uncertain significance ★★ ⚠ same condition
TKFC p.Asp403Asn Uncertain significance ★★ ⚠ same condition
TKFC c.194-13C>T Benign ★★ same condition
TKFC c.775+39A>C Benign ★★ same condition
TKFC p.Ala185Thr Benign ★★ same condition
TKFC p.Thr157= Benign ★★ same condition
TKFC p.Val437= Benign ★★ 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/tkfc-p-asp43fs (accessed [today's date]).

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