Is FLT4 p.Lys563= (c.1689G>A) pathogenic?

FLT4 p.Lys563= (c.1689G>A) is classified Likely benign in FLT4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-05-26). Absent from gnomAD v4.1; Associated with FLT4-related disorder.

What condition is associated with FLT4 p.Lys563= (c.1689G>A)?

FLT4 p.Lys563= (c.1689G>A) is associated with FLT4-related disorder (ClinVar).

How common is FLT4 p.Lys563= (c.1689G>A) in the general population?

FLT4 p.Lys563= (c.1689G>A) is absent from gnomAD v4.1 (gnomAD).

FLT4 p.Lys563=

c.1689G>A · rs2480926279 · VCV3061693

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

FLT4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.22	GERP -2.6, phastCons 0.97
Overall
CADD	2.731	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FLT4
Protein: p.Lys563=
Coding: c.1689G>A
MANE Select: NM_182925
dbSNP: rs2480926279
Type: single nucleotide variant
Location: chr5:180621873 (GRCh38)
Gene constraint: LOEUF 0.265 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.82 · 2 PDB
Residue 563: the ig-like c2-type 6 domain; a UniProt-annotated variant site (in chtd7)

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

Disease context

FLT4-related disorder

Similar variants

FLT4 p.Lys563Arg Uncertain significance ★ ⚠ same residue
FLT4 p.Gly857Arg Pathogenic ★★ same condition
FLT4 p.Pro1137Leu Likely pathogenic ★★ same condition
FLT4 p.Ser393Arg Uncertain significance ★★ ⚠ same condition
FLT4 c.2168-1G>A Likely pathogenic ★ same condition
FLT4 p.Arg1041Gly Likely pathogenic ★ same condition
FLT4 p.Gln1020Leu Pathogenic ★ same condition
FLT4 p.Gln1179Ter 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/flt4-p-lys563 (accessed [today's date]).

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