Is FLT4 p.Asn799fs (c.2396del) pathogenic?

FLT4 p.Asn799fs (c.2396del) is classified Likely pathogenic in FLT4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-01). Absent from gnomAD.

How common is FLT4 p.Asn799fs (c.2396del) in the general population?

FLT4 p.Asn799fs (c.2396del) is absent from gnomAD (gnomAD).

FLT4 p.Asn799fs

c.2396del · rs2480904044 · VCV3234777

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

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 16 of 30
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP -3.2, 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: FLT4
Protein: p.Asn799fs
Coding: c.2396del
MANE Select: NM_182925
dbSNP: rs2480904044
Type: Deletion
Location: chr5:180620619 (GRCh38)
Gene constraint: LOEUF 0.265 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.82 · 2 PDB
Residue 799: a UniProt-annotated variant site (in chtd7)

Full FLT4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FLT4 p.Glu100fs Pathogenic/Likely pathogenic ★★ same type
FLT4 c.1421+19_1421+37del Benign ★★ same type
FLT4 c.3220-35_3220-2del Benign/Likely benign ★★ same type
FLT4 p.Arg642fs Likely pathogenic ★ same type
FLT4 p.Asn538fs Likely pathogenic ★ same type
FLT4 p.Gly744fs Likely pathogenic ★ same type
FLT4 p.Gly854fs Pathogenic ★ same type
FLT4 p.Gly975fs 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/flt4-p-asn799fs (accessed [today's date]).

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