Is KIT p.Arg796Gly (c.2386A>G) pathogenic?

KIT p.Arg796Gly (c.2386A>G) is classified Pathogenic in KIT (ClinVar, No assertion criteria, 1 submitter; last evaluated 1998-01-06). AlphaMissense: likely pathogenic (0.9995); Absent from gnomAD v4.1; Associated with Piebaldism with sensorineural deafness.

What condition is associated with KIT p.Arg796Gly (c.2386A>G)?

KIT p.Arg796Gly (c.2386A>G) is associated with Piebaldism with sensorineural deafness (ClinVar).

How common is KIT p.Arg796Gly (c.2386A>G) in the general population?

KIT p.Arg796Gly (c.2386A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about KIT p.Arg796Gly (c.2386A>G)?

AlphaMissense predicts likely pathogenic (score 0.9995) — an in-silico prediction, not a clinical call.

KIT p.Arg796Gly

c.2386A>G · rs121913684 · VCV13858

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9995 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Piebaldism with sensorineural deafness

Computational evidence

Protein change
AlphaMissense	0.9995	likely pathogenic ✓ concordant with ClinVar · top 4% in KIT
REVEL	0.835	moderately pathogenic-leaning
SaProt	LLR -16.23	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.9	GERP -2.5, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 4,810 bp · p 2.2e-10 · regional, not allelic
Overall
CADD	26.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: KIT
Protein: p.Arg796Gly
Coding: c.2386A>G
MANE Select: NM_000222
dbSNP: rs121913684
Type: single nucleotide variant
Location: chr4:54733094 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 796: the protein kinase domain; a binding site; an α-helix; a UniProt-annotated variant site (in pbt; with sensorineural deafness)

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

Disease context

Piebaldism with sensorineural deafness — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same type
KIT p.Asp816His Pathogenic ★★ same type
KIT p.Asp820Tyr Pathogenic ★★ same type
KIT p.Gln190Ter Pathogenic ★★ same type
KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same type
KIT p.Lys642Glu Pathogenic ★★ same type
KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same type
KIT p.Val559Ala Pathogenic/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/kit-p-arg796gly (accessed [today's date]).

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