Is KIT p.Ser771= (c.2313C>T) pathogenic?

KIT p.Ser771= (c.2313C>T) is classified Likely benign in KIT (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-05). Very rare (popmax 0.000339%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with KIT p.Ser771= (c.2313C>T)?

KIT p.Ser771= (c.2313C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is KIT p.Ser771= (c.2313C>T) in the general population?

KIT p.Ser771= (c.2313C>T) is very rare (popmax 0.000339%, nfe) (gnomAD).

KIT p.Ser771=

c.2313C>T · rs2475565299 · VCV1789469

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000339%, 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 1.4	GERP 1.7, phastCons 1
Overall
CADD	9.535	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,179,736 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000248% 4/1,613,368 alleles · very rare exomes 4/1,461,564 · genomes 0/151,804 · joint denominator

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.Ser771=
Coding: c.2313C>T
MANE Select: NM_000222
dbSNP: rs2475565299
Type: single nucleotide variant
Location: chr4:54731950 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 771: the protein kinase domain; an α-helix

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

Similar variants

KIT p.Ser771Asn Uncertain significance ★★ ⚠ same residue
KIT p.Ser771Cys Uncertain significance ★ ⚠ same residue
KIT p.Ser771Gly Uncertain significance ★ ⚠ same residue
KIT p.Asp820Tyr Pathogenic ★★ same condition
KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same condition
KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same condition
KIT p.Val559Ala Pathogenic/Likely pathogenic ★★ same condition
KIT c.1232-3T>C Uncertain significance ★★ 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-ser771 (accessed [today's date]).

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