KIT c.1669_1674del, p.Trp557_Lys558del

Reasoning

PS3 is met at strong strength. The exact KIT p.(Trp557_Lys558del) variant was tested in stable engineered Ba/F3 functional systems. In PMID:17699867, KITWK557-8del cells showed drug-responsive abnormal KIT-dependent growth, with inhibition by imatinib, dasatinib, sorafenib, and nilotinib, apoptosis after dasatinib or nilotinib, and reported IC50 values of 460, 58, 211, and 83 nmol/L, respectively. In PMID:25239608, the exact exon 11 Δ557-558 mutant was tested in KIT-dependent Ba/F3 viability assays and in vivo xenografts; ponatinib produced a dose-dependent antitumor effect and near-complete regression at 30 mg/kg. These are variant-specific, orthogonal in vitro and in vivo functional studies in a biologically relevant KIT/GIST model and support an activating, damaging effect. PMID:15930355 independently reports weak KIT phosphorylation limited to the mature isoform in three untreated GISTs carrying the identical deletion, providing additional biological relevance, although it is not itself a standalone functional calibration study. The evidence is strong but is not described as validated and reproducible in a clinical diagnostic laboratory setting.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• PMID:17699867, Results/Table 1/Figures 1–2: stable Ba/F3 cells expressing KITWK557-8del were evaluated by proliferation, apoptosis, and KIT-phosphorylation assays; growth was inhibited by imatinib, dasatinib, sorafenib, and nilotinib, with IC50 values of 460, 58, 211, and 83 nmol/L, respectively.
• PMID:25239608, Results and in vivo studies: engineered KIT-dependent Ba/F3 assays included the exon 11 Δ557-558 mutant, and xenografts carrying KIT exon 11 Δ557-558 showed dose-dependent ponatinib antitumor activity with near-complete regression at 30 mg/kg.
• PMID:15930355, Table 1/Table 2/Results: the identical 557-8 WK deletion was observed as a primary KIT mutation in three GIST patients, and all three untreated GISTs showed weak phosphorylation limited to the mature KIT isoform.
• Strength calibration: the exact variant is supported by multiple orthogonal cellular and in vivo assays in relevant KIT-dependent models, but the extracted evidence does not establish clinical diagnostic-laboratory validation or reproducibility; strong rather than very strong evidence is therefore assigned.

Sources

Reasoning

PM2 is met at supporting strength. The exact KIT NM_000222.3:c.1669_1674del variant is absent from gnomAD v2.1 and gnomAD v4.1, including the available non-cancer subset checks. Under the generic rule, this is absence from controls and satisfies the supplied PM2 supporting threshold of <=0.0001. No VCEP specifies an alternative population source. The indel calling caveat warrants ordinary caution, but concordant absence across the available datasets supports the criterion.

Rule

PM2: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium ... PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)

Evidence considered

• gnomAD v2.1 reports the exact KIT NM_000222.3:c.1669_1674del variant as absent; the non-cancer subset check also reports absence.
• gnomAD v4.1 reports the exact KIT NM_000222.3:c.1669_1674del variant as absent; the non-cancer subset check also reports absence.
• The generic PM2 supporting threshold supplied for this case is <=0.0001; absence corresponds to an observed allele frequency of 0 and is below that threshold.
• The ACMG/AMP caveat notes that population data for indels may be poorly called by next generation sequencing; the concordant absence in both available gnomAD releases reduces, but does not eliminate, this technical concern.

Sources

Reasoning

NM_000222.3:c.1669_1674del is an exact six-base in-frame deletion in the MANE Select KIT transcript, producing NP_000213.1:p.(Trp557_Lys558del) and removing two amino acids without altering the reading frame. The deletion is in KIT exon 11 within the juxtamembrane region, not a documented repetitive region, and variant-specific studies describe it as an exon 11 activating deletion in patient tumors and engineered cellular or xenograft models. Therefore it is a protein-length change meeting PM4; no NMD consideration applies because this is an in-frame deletion rather than a premature termination variant.

Rule

Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.

Evidence considered

• Variant normalization identifies NM_000222.3:c.1669_1674del as NP_000213.1:p.(Trp557_Lys558del), an in-frame two-residue deletion in exon 11 of the MANE Select KIT transcript.
• Molecular and clinical tumor data explicitly report the exact deletion as KIT exon 11 WK557-558del in a GIST cohort; the study used KIT exon sequencing and follow-up molecular analyses in 31 patients.
• Variant-specific Ba/F3 assays studied KITWK557-8del, and the exact deletion was also evaluated in engineered KIT-dependent cellular and xenograft models as an activating exon 11 deletion.
• The evidence places the deletion in KIT exon 11 and the juxtamembrane region; no evidence identifies the affected sequence as a repetitive region without known function.

Sources

Reasoning

The exact variant is reported in affected GIST patients, including three patients in a 31-patient imatinib-treated cohort and one patient in a 147-patient advanced-GIST cohort, but the reviewed literature provides no unaffected or population-control carrier count, matched-ancestry gnomAD carrier frequency, case-control comparison, odds ratio, relative risk, or confidence interval. The PS4 rule requires an affected-versus-control prevalence increase and, under the supplied ACMG/AMP note, OR or RR >5.0 with a confidence interval excluding 1.0; no such comparison can be calculated. The literature_pass PS4 lead (PMID:25394175) was checked in its full-text extraction and does not mention this variant or provide variant-specific case-control evidence.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.

Evidence considered

• PMID:15930355, Table 1 patients #10 and Table 2 patients #19 and #28: the exact WK557-558del was present as a primary KIT exon 11 mutation in three affected GIST patients; no unaffected/control comparison was reported.
• PMID:16954519, Table 2 Patient 2: the exact KIT exon 11 Del WK557-558 was present in one affected GIST patient; no unaffected/control comparison was reported.
• PMID:25394175 full-text extraction: the paper does not mention KIT c.1669_1674del or p.(W557_K558del) and supplies no variant-specific case-control data.
• The required PS4 comparison was not computable: no case/control counts or matched-ancestry control frequency were available, so no OR/RR or 95% CI could be calculated.

Still missing

• Variant-specific unaffected or population-control carrier counts, or a matched-ancestry control frequency, are unavailable; therefore OR/RR and its 95% CI cannot be calculated.

Sources

Reasoning

ClinVar contains an exact-variant Likely pathogenic submission, but its review status is criteria provided, single submitter, with zero expert-panel submissions. The supplied PP5 rule requires a reputable source to report the variant as pathogenic while evidence is unavailable for independent evaluation; under the instructed generic rule, an ordinary laboratory submission, aggregate label, or non-expert assertion cannot trigger PP5. The literature_pass PP5 lead (PMID:25394175) was verified in its extraction and does not mention this variant.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 222957: exact variant NM_000222.3(KIT):c.1669_1674del (p.Trp557_Lys558del) is Likely pathogenic with review status criteria provided, single submitter; expert-panel submissions = 0.
• PMID:25394175 full-text extraction: the paper does not mention KIT c.1669_1674del or p.(W557_K558del), so it cannot independently support PP5.

Sources

Reasoning

BA1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, so no qualifying grpmax filtering allele frequency (FAF) is reported; an absent variant cannot reach the generic BA1 threshold of >= 0.05. The generic stand-alone benign threshold is therefore not met. No small-population popmax point estimate or ancestry-specific frequency is available to override this conclusion.

Rule

BA1: Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium ... BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)

Evidence considered

• gnomAD v2.1 reports the exact KIT NM_000222.3:c.1669_1674del variant as absent.
• gnomAD v4.1 reports the exact KIT NM_000222.3:c.1669_1674del variant as absent.
• Because the variant is absent, no grpmax filtering allele frequency (FAF) is available; the generic BA1 threshold is >= 0.05, and no popmax point estimate is substituted for FAF.

Sources

Reasoning

BS1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, so no grpmax filtering allele frequency (FAF) is reported and the generic default threshold of >=0.01 is not reached. There is no ancestry-specific elevation, founder signal, or frequency metric requiring a maximum-credible-allele-frequency calculation.

Rule

BS1: Allele frequency is greater than expected for the disorder ... BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)

Evidence considered

• gnomAD v2.1 reports the exact KIT NM_000222.3:c.1669_1674del variant as absent.
• gnomAD v4.1 reports the exact KIT NM_000222.3:c.1669_1674del variant as absent.
• The generic BS1 default is >=0.01, but no grpmax filtering allele frequency (FAF) is available because the variant is absent; no popmax point estimate is used.

Sources

Reasoning

The variant is an in-frame deletion, but the available evidence does not place it in a repetitive region without a known function. Instead, NM_000222.3:c.1669_1674del produces p.(Trp557_Lys558del) in KIT exon 11's functionally important juxtamembrane region, and variant-specific clinical and experimental studies describe this deletion as an activating KIT alteration. It therefore does not meet the BP3 requirement.

Rule

In frame-deletions/insertions in a repetitive region without a known function.

Evidence considered

• Variant normalization identifies NM_000222.3:c.1669_1674del as NP_000213.1:p.(Trp557_Lys558del) in KIT exon 11.
• The exact deletion is reported as an exon 11 WK557-558 deletion in patient tumors and as an activating deletion in variant-specific Ba/F3 and xenograft studies.
• The available evidence supports a known functional KIT juxtamembrane context and provides no evidence that the deleted sequence is a repetitive region without known function.

Sources

Reasoning

No exact-variant ClinVar expert-panel classification as benign or likely benign is present. ClinVar instead shows a single-submitter Likely pathogenic laboratory assertion and a non-criteria Likely oncogenic somatic submission, with zero expert-panel submissions. Under the instructed generic rule, these records cannot trigger BP6.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 222957: exact-variant records include one single-submitter Likely pathogenic laboratory assertion and one no-criteria Likely oncogenic somatic submission; expert-panel submissions = 0, and no benign or likely benign expert-panel classification is present.

Sources

Reasoning

PS2 cannot be assessed because the available case evidence does not document a proband-level disease phenotype, absence of family history, or confirmed maternity and paternity for this variant. The extracted variant publications describe somatic GIST tumor cohorts and do not provide germline trio testing or de novo evidence.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• PMID:15930355 reports the variant in primary KIT mutations from a 31-patient somatic GIST treatment cohort, without germline trio testing or de novo assessment.
• PMID:16954519 reports the variant in a somatic GIST patient tumor cohort, without germline parental testing or de novo assessment.
• The supplied case records contain no documented proband phenotype, family history, confirmed maternity, confirmed paternity, or parental variant results.

Still missing

• Document the proband's phenotype and disease diagnosis.
• Document family history relevant to the disease.
• Provide molecular confirmation of both maternity and paternity and parental absence of the variant.

Sources

Reasoning

PM3 cannot be assessed because the available evidence concerns somatic KIT exon 11 alterations in GIST tumors and does not establish a recessive inherited disorder, an affected proband with the queried allele, a pathogenic variant in trans, or parent/offspring testing to determine phase. The variant-specific reports describe tumor genotypes and treatment or functional results, not germline allelic observations.

Rule

PM3: For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.

Evidence considered

• PMID:15930355, Table 1 patients #10 and Table 2 patients #19 and #28: the queried WK557-558del is reported as a primary tumor KIT mutation in GIST; no germline, parent/offspring, or phase data are reported.
• PMID:16954519, Table 2 patient 2: the queried Del WK557-558 is reported as a primary tumor KIT mutation; no germline inheritance or phase data are reported.
• PMID:17699867 and PMID:25239608: variant-specific engineered-cell and xenograft experiments evaluate KIT activity or drug response, not allelic phase or inheritance.
• No source in the reviewed case evidence documents a recessive inherited KIT disorder, an affected germline proband, or a pathogenic variant demonstrated in trans.

Still missing

• Establish whether the relevant disorder is recessive and inherited.
• Document an affected proband carrying the queried variant and a pathogenic variant in trans.
• Obtain parental or offspring testing to determine phase.

Sources

Reasoning

PM6 cannot be assessed because the available case evidence does not document an assumed de novo occurrence in a patient with the relevant disease. No proband phenotype, family history, or parental testing results are provided; the extracted variant publications concern somatic tumor cohorts.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• PMID:15930355 reports the variant in somatic GIST tumors and does not report a germline de novo assessment.
• PMID:16954519 reports the variant in a somatic GIST tumor cohort and does not report parental testing or de novo origin.
• The supplied case records contain no documented patient-level phenotype, family history, or parental testing results for this variant.

Still missing

• Document the proband's phenotype and disease diagnosis.
• Document the family history.
• Provide evidence that the variant was absent from tested parents or explain the basis for assuming de novo origin.

Sources

Reasoning

PP1 cannot be assessed because no affected family members, familial genotypes, phenotype concordance, or informative meioses are documented. The available variant publications report somatic GIST cohorts rather than familial segregation studies.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... Note: May be used as stronger evidence with increasing segregation data.

Evidence considered

• PMID:15930355 describes three somatic GIST patients with the deletion but provides no familial segregation or affected-relative analysis.
• PMID:16954519 describes a somatic GIST patient with the deletion but provides no familial segregation or affected-relative analysis.
• The supplied case records contain no family structure, affected-relative phenotypes, familial genotypes, or meiosis count.

Still missing

• Identify affected relatives and document their disease phenotypes.
• Provide variant testing results for affected and unaffected relatives.
• Provide the number of informative meioses and assess phenotype consistency.

Sources

Reasoning

The supplied case evidence identifies the variant and literature reports in GIST tumors, but it does not provide the patient's phenotype, family history, or a sufficiently specific clinical presentation to evaluate whether the phenotype is highly specific for a single-gene disease etiology. The governing PP4 definition therefore cannot be applied from the available case-level evidence.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• The available case materials provide variant normalization and tumor/literature observations but no patient phenotype or family-history description suitable for PP4 assessment.

Still missing

• Patient phenotype and family-history details, including whether the presentation is highly specific for a single KIT-related disease etiology, are unavailable.

Reasoning

BS2 cannot be assessed from the supplied evidence. No individual-level observation documents this exact variant in a healthy adult, and the gnomAD records provide no phenotypic, age, penetrance, or clinical follow-up information. Zero reported homozygotes in gnomAD do not establish or exclude BS2. The required early-age full-penetrance applicability of the generic definition is also not documented for the KIT-associated gastrointestinal stromal tumor context.

Rule

BS2: Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• The available gnomAD v2.1 and v4.1 records report the variant as absent and provide no individual phenotype, age, penetrance, or clinical follow-up data.
• No supplied clinical or research source documents a healthy adult carrying this exact variant.

Still missing

• Individual-level, phenotyped healthy adult observation of the exact variant, including age, disease status, inheritance state, and follow-up, is needed.
• The expected penetrance and age of onset for the governing KIT-associated disorder need confirmation before applying BS2.

Sources

Reasoning

BS3 is not assessed because the available studies do not establish that the exact KIT p.(Trp557_Lys558del) variant has no damaging effect on protein function or splicing. The available variant-specific assays instead show KIT-dependent cellular and xenograft behavior consistent with an activating effect, and no well-established benign functional or splicing assay with appropriate normal controls was identified.

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• PMID:17699867 and PMID:25239608 provide variant-specific functional assays, but their results are consistent with altered KIT activity and do not support a benign BS3 interpretation.
• No available study provides a validated normal-function or normal-splicing result for KIT p.(Trp557_Lys558del) with sufficient controls for BS3.

Still missing

• A well-established variant-specific assay demonstrating no damaging effect on KIT protein function or splicing, with appropriate normal and disease-positive controls, is unavailable.

Sources

Reasoning

BS4 cannot be assessed because the available case evidence does not identify affected family members who were tested and did not carry the variant. No familial non-segregation data are reported, and therefore the phenocopy and multiple-pathogenic-variant caveats cannot be evaluated.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• No affected-relative testing or familial non-segregation result is documented in the supplied case records.
• The available variant publications report somatic GIST cohorts and do not provide affected-family-member testing relevant to BS4.

Still missing

• Identify affected relatives and document their diagnoses.
• Provide variant test results for affected relatives.
• Evaluate possible phenocopies and the possibility of more than one pathogenic variant in the family.

Sources

Reasoning

BP2 cannot be assessed because the available evidence does not document a second pathogenic variant in trans or cis with the queried variant, does not establish a fully penetrant dominant inherited KIT disorder, and provides no parental, offspring, tumor-clone, or other phasing result. The available publications report the queried variant as a primary somatic KIT alteration or study it experimentally, without allelic observations required for BP2.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• PMID:15930355: the queried WK557-558del is reported in three GIST tumors, with secondary T670I reported in one patient and no documented cis/trans relationship to the queried deletion.
• PMID:16954519: the queried Del WK557-558 is reported with a secondary Y823D mutation in a progression sample, but no phase relationship is established.
• PMID:17699867 and PMID:25239608: experimental constructs and xenograft models include the queried deletion with secondary mutations in some assays, but the cited extracts do not establish cis/trans phase for a clinical specimen.
• No reviewed source documents the queried variant in cis or trans with a pathogenic variant under a qualifying dominant or other inheritance context.

Still missing

• Identify a pathogenic variant paired with the queried variant in the same individual or tumor sample.
• Determine whether the variants are in cis or trans using parental, offspring, clone, or other validated phasing data.
• Establish whether a fully penetrant dominant KIT disorder is the relevant disease context if a trans observation is proposed.

Sources

Reasoning

The available evidence shows the exact variant in GIST tumors, but it does not document a case with an alternate molecular basis for disease, such as a confirmed pathogenic alternative variant or another established molecular cause in the same case. BP5 therefore cannot be assessed from the available case-level evidence.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• The reviewed GIST reports describe the KIT variant and tumor mutations but do not establish an alternate molecular basis for disease in the relevant case.

Still missing

• A case-level confirmed alternate molecular diagnosis is unavailable.

Sources