4-54733155-A-T

Variant names:

• chr4-54733155-A-T
• rs121913507
• NM_000222.3:c.2447A>T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PM5 PP2 PP3_Strong PP5

The NM_000222.3(KIT):​c.2447A>T​(p.Asp816Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D816F) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: KIT NM_000222.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:4 O:1
• Conservation: PhyloP100: 9.22

Genes affected

KIT (HGNC:6342): (KIT proto-oncogene, receptor tyrosine kinase) This gene encodes a receptor tyrosine kinase. This gene was initially identified as a homolog of the feline sarcoma viral oncogene v-kit and is often referred to as proto-oncogene c-Kit. The canonical form of this glycosylated transmembrane protein has an N-terminal extracellular region with five immunoglobulin-like domains, a transmembrane region, and an intracellular tyrosine kinase domain at the C-terminus. Upon activation by its cytokine ligand, stem cell factor (SCF), this protein phosphorylates multiple intracellular proteins that play a role in in the proliferation, differentiation, migration and apoptosis of many cell types and thereby plays an important role in hematopoiesis, stem cell maintenance, gametogenesis, melanogenesis, and in mast cell development, migration and function. This protein can be a membrane-bound or soluble protein. Mutations in this gene are associated with gastrointestinal stromal tumors, mast cell disease, acute myelogenous leukemia, and piebaldism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• PP2: Missense variant in the KIT gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 54 curated pathogenic missense variants (we use a threshold of 10). The gene has 7 curated benign missense variants. Gene score misZ: 2.5806 (below the threshold of 3.09). Trascript score misZ: 4.1549 (above the threshold of 3.09). GenCC associations: The gene is linked to piebaldism, gastrointestinal stromal tumor, mastocytosis, cutaneous mastocytosis.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.983
• PP5: Variant 4-54733155-A-T is Pathogenic according to our data. Variant chr4-54733155-A-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 13852.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=4, Pathogenic=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIT	NM_000222.3	c.2447A>T	p.Asp816Val	missense_variant	Exon 17 of 21	ENST00000288135.6	NP_000213.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIT	ENST00000288135.6	c.2447A>T	p.Asp816Val	missense_variant	Exon 17 of 21	1	NM_000222.3	ENSP00000288135.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1460592 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 726630

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000468 Hom.: 0

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:4 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Cutaneous mastocytosis Pathogenic:2 Uncertain:1

-

Neuberg Centre For Genomic Medicine, NCGM

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The missense c.2447A>T p.Asp816Val variant in KIT gene has been reported repviously as the most common somatic variant causing systemic mastocytosis Ke et al. 2016; Nedoszytko et al. 2021. Experimental studies show that this variant leads to an ligand-independent activation and it gains extra activity via different signaling pathways from that of wild-type KIT Ke et al. 2016. The p.Asp816Val variant is reported with an allele frequency of 0% i.e. no high-confidence genotypes in the gnomAD exomes database and is novel not in any individuals in 1000 Genomes database. The frequency data for this variant in gnomAD exomes database is considered unreliable, as metrics indicate poor data quality at this position. This variant has been reported to the ClinVar database Uncertain Significance / Likely Pathogenic / Pathogenic. The amino acid change p.Asp816Val in KIT is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Asp at position 816 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -

Aug 31, 2021

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS3 supporting, PM2 moderate, PP3 supporting -

Aug 15, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Gastrointestinal stromal tumor Uncertain:2

Nov 01, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 816 of the KIT protein (p.Asp816Val). This variant is not present in population databases (gnomAD no frequency). This variant is the most common somatic change in mastocytosis (PMID: 27777718, 26158763). While this variant has been reported in the literature, it has not been reported in the germline of individuals with KIT-related conditions. ClinVar contains an entry for this variant (Variation ID: 13852). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this variant leads to a gain-of-function of the KIT protein, causing ligand-independent signaling activation as well as oncogenic transformation in vitro (PMID: 27777718, 26158763). In addition, transgenic mice expressing this variant (D816V) show abnormal mast cell proliferation and recapitulate human mastocytosis (PMID: 16352739). However, the clinical significance of the functional impact in the germline is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Mar 28, 2024

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

MAST CELL LEUKEMIA, SOMATIC Pathogenic:1

Aug 15, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:1

Nov 24, 2014

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

MASTOCYTOSIS, SYSTEMIC, SOMATIC Pathogenic:1

Aug 15, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

MASTOCYTOSIS WITH ASSOCIATED HEMATOLOGIC DISORDER, SOMATIC Pathogenic:1

Aug 15, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Hereditary cancer-predisposing syndrome Uncertain:1

Jan 30, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.D816V variant (also known as c.2447A>T), located in coding exon 17 of the KIT gene, results from an A to T substitution at nucleotide position 2447. The aspartic acid at codon 816 is replaced by valine, an amino acid with highly dissimilar properties. This variant is the most common somatic alteration reported in adults with acquired mastocytosis (Arock M et al. Leukemia 2015 Jun;29(6):1223-32; Orfao A et al. Br. J. Haematol. 2007 Jul;138(1):12-30; Nagata H et al. Proc. Natl. Acad. Sci. U.S.A. 1995 Nov;92(23):10560-4; Baird J et al. Curr Hematol Malig Rep 2018 10;13(5):407-416). Functional studies have demonstrated that p.D816V leads to constitutive activation of KIT (Foster R et al. J. Mol. Graph. Model. 2004 Oct;23(2):139-52; Nagata et al). To our knowledge, p.D816V has not yet been identified as a germline alteration and has not been established to confer increased risk of familial gastrointestinal stromal tumors (GIST). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. -

Dysgerminoma Other:1

May 01, 2016

Donald Williams Parsons Laboratory, Baylor College of Medicine

Significance: other

Review Status: no assertion criteria provided

Collection Method: clinical testing

- 2: Mutations in members of targetable cancer pathways, gene families, or functional groups, regardless of tumor type;

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	30
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.80	.;D
Eigen	Uncertain	0.65
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D;D
M_CAP	Uncertain	0.18	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Uncertain	0.30	D
MutationAssessor	Benign	0.095	.;N
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-7.5	D;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Polyphen		1.0	D;D
Vest4		0.97
MutPred		0.89		.;Gain of MoRF binding (P = 0.0494);
MVP		0.99
MPC		1.6
ClinPred		1.0	D
GERP RS		5.6
Varity_R		0.95
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121913507; hg19: chr4-55599321; COSMIC: COSV55386424;