Is KIT p.Ile798= (c.2394C>T) pathogenic?

KIT p.Ile798= (c.2394C>T) is classified Benign/Likely benign in KIT (ClinVar, Multiple submitters, 17 submitters; last evaluated 2026-06-04). Low-frequency (popmax 3.4%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with KIT p.Ile798= (c.2394C>T)?

KIT p.Ile798= (c.2394C>T) is associated with hereditary neoplastic syndrome, mastocytosis, piebaldism (ClinVar).

How common is KIT p.Ile798= (c.2394C>T) in the general population?

KIT p.Ile798= (c.2394C>T) is low-frequency (popmax 3.4%, nfe) (gnomAD).

KIT p.Ile798=

c.2394C>T · rs55789615 · VCV255571

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 17 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.4%, nfe)

Conditions

hereditary neoplastic syndrome

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 0.6	GERP -1.3, phastCons 1
Overall
CADD	8.772	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.4% European (non-Finnish) · 40,011/1,177,766 alleles

Filtering AF 3.37% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.36%

Overall 2.82% 45,436/1,611,398 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	18.2%	5
European (non-Finnish)grpmax	3.4%	29
Middle Eastern	2.66%	38
Remaining individualsnot grpmax-eligible	2.34%	43
Ashkenazi Jewishnot grpmax-eligible	2.05%	49
Finnishnot grpmax-eligible	1.38%	73
Admixed American	1.3%	77
South Asian	1.06%	94
African / African-American	0.531%	188
East Asian	0.00669%	14,937

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: KIT
Protein: p.Ile798=
Coding: c.2394C>T
MANE Select: NM_000222
dbSNP: rs55789615
Type: single nucleotide variant
Location: chr4:54733102 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 798: the protein kinase domain; a β-strand

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: mastocytosis piebaldism gastrointestinal stromal tumor

Similar variants

KIT p.Ile798Thr Uncertain significance ★★ ⚠ same residue
KIT p.Ile798Val Uncertain significance ★ ⚠ same residue
KIT p.Ile798_Gly803delinsSer Uncertain significance ★ same residue
KIT p.Ile798Phe Likely pathogenic ★ same residue
KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same condition
KIT p.Asp820Tyr Pathogenic ★★ same condition
KIT p.Gln190Ter Pathogenic ★★ same condition
KIT p.Leu576Pro Pathogenic/Likely 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/kit-p-ile798 (accessed [today's date]).

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