Is KDR p.Lys941= (c.2823A>G) pathogenic?

KDR p.Lys941= (c.2823A>G) is classified Likely benign in KDR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-10). Ultra-rare (popmax 0.0133%, amr); Associated with KDR-related disorder.

What condition is associated with KDR p.Lys941= (c.2823A>G)?

KDR p.Lys941= (c.2823A>G) is associated with KDR-related disorder (ClinVar).

How common is KDR p.Lys941= (c.2823A>G) in the general population?

KDR p.Lys941= (c.2823A>G) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

KDR p.Lys941=

c.2823A>G · rs772654881 · VCV3046459

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

Conditions

KDR-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 1.2	GERP 0.6, phastCons 1
Overall
CADD	8.764	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% Admixed American · 8/60,016 alleles

Filtering AF 0.00661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00482%

Overall 0.000547% 8/1,461,568 alleles · ultra-rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: KDR
Protein: p.Lys941=
Coding: c.2823A>G
MANE Select: NM_002253
dbSNP: rs772654881
Type: single nucleotide variant
Location: chr4:55094950 (GRCh38)
Gene constraint: LOEUF 0.328 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.67 · 54 PDB
Residue 941: the protein kinase domain

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

Disease context

KDR-related disorder

Similar variants

KDR p.Gly1092Arg Uncertain significance ⚠ same condition
KDR c.1537-6G>A Likely benign same condition
KDR c.3510+10C>T Likely benign same condition
KDR c.-1G>T Benign same condition
KDR p.Gln472His Benign same condition
KDR p.Gly1283= Likely benign same condition
KDR p.Ile1330Leu Benign same condition
KDR p.Pro956= Likely 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/kdr-p-lys941 (accessed [today's date]).

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