NM_002529.3:c.1999G>A

NTRK1 · NP_002520.2:p.(Gly667Ser) · NM_002529.3

GRCh37: chr1:156849107 G>A · GRCh38: chr1:156879315 G>A

Gene: NTRK1 Transcript: NM_002529.3

Final call

VUS

PM1 moderate PM2 moderate

Variant details

Gene

NTRK1

Transcript

NM_002529.3

Protein

NP_002520.2:p.(Gly667Ser)

gnomAD AF

ClinVar

OncoKB

Inconclusive

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_002529.3:c.1999G>A (p.Gly667Ser) is a novel missense variant in the NTRK1 gene. It is absent from population databases (gnomAD v2.1, v4.1, gnomAD-Canada; PM2) and is located in the functionally critical xDFG motif of the tyrosine kinase domain immediately N-terminal to the DFG activation loop (PM1). In silico data from two publications (PMID:33004339, PMID:33328556) demonstrate altered kinase inhibitor binding for G667S by molecular docking and molecular dynamics simulations, and G667S has been observed as an acquired somatic resistance mutation in two patients with TRK fusion-positive cancers on larotrectinib therapy (PMID:33004339). No experimental functional characterization of G667S exists, and the variant has not been reported in ClinVar. In silico predictors are discordant (REVEL 0.752, BayesDel 0.262).

Two moderate pathogenic criteria are met (PM1, PM2). Under the generic ACMG/AMP 2015 framework (Richards et al., PMID:25741868), this does not reach the threshold for Likely Pathogenic (which requires ≥3 moderate criteria, or ≥1 strong + ≥1 moderate, or ≥2 moderate + ≥2 supporting). No benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_002529.3:c.1999G>A is a missense variant (p.Gly667Ser). It does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. PVS1 is not applicable to missense variants under the ClinGen SVI PVS1 framework (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	N/A	No known pathogenic missense variant at codon 667 producing the same amino acid change (p.Gly667Ser) via a different nucleotide change has been identified. This variant is absent from ClinVar, and no alternate nucleotide substitution at this codon yielding p.Gly667Ser has been reported as pathogenic.	clinvar pm5_candidates
PS2	Not met	No de novo observation data are available for this variant. No reports of de novo occurrence with confirmed parentage were identified in the case materials or literature.
PS3	Not met	No experimental functional data exist for NM_002529.3:c.1999G>A (p.G667S) relevant to germline disease mechanism. PMID:33004339 includes G667S in molecular dynamics simulations (in silico modeling) and reports its emergence as a somatic resistance mutation in two patients with TRK fusion-positive cancers on larotrectinib, but no wet-lab functional assay (kinase assay, reporter assay, or other experimental characterization) was performed specifically on G667S. PMID:33328556 provides molecular docking dissociation constants for G667S (in silico only). Computational predictions do not satisfy PS3 requirements for experimental functional evidence. The somatic resistance context does not inform germline NTRK1 loss-of-function pathogenicity for CIPA.	PMID:33004339 PMID:33328556
PS4	Not met	No case-control or cohort data comparing variant prevalence in affected individuals versus controls are available. The variant has been observed as a somatic resistance mutation in two cancer patients (PMID:33004339), but this does not constitute germline case-control evidence for PS4.
PS5	N/A	PS5 is not a standard ACMG/AMP 2015 criterion and is not defined in the generic ACMG classification framework used for this assessment. No VCEP-specific PS5 rule exists for NTRK1.	generic_acmg_combination_rules final_classification_framework
PM1	Met	The variant alters Gly667, which is the xDFG residue immediately N-terminal to the DFG motif (Asp668-Phe669-Gly670) in the activation loop of the NTRK1 tyrosine kinase domain. The DFG motif is a critical, evolutionarily conserved structural element that governs kinase conformational state (DFG-in active vs DFG-out inactive). PMID:33004339 demonstrates that xDFG substitutions at G667 (including G667S) emerge as clinical resistance mutations to type I TRK inhibitors and alter kinase-inhibitor interactions via in silico modeling. PMID:33328556 confirms altered drug binding for G667S across five kinase inhibitors by molecular docking. This residue lies within a well-characterized, functionally critical domain without known benign variation.	PMID:33004339 PMID:33328556 pvs1_gene_context
PM2	Met	NM_002529.3:c.1999G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). The variant has not been observed in any population database, consistent with PM2 at the <0.1% allele frequency threshold for a rare disease gene.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No missense variant at codon 667 resulting in a different amino acid substitution has been classified as germline pathogenic in ClinVar. G667C has been reported as a somatic resistance mutation in TRK fusion-positive cancers (PMID:33004339, PMID:33328556) but is not classified as germline pathogenic. The PM5 candidate search found zero same-residue comparator variants in ClinVar.	pm5_candidates clinvar PMID:33004339 PMID:33328556
PM6	Not met	No de novo observation data are available. PM6 (assumed de novo without confirmation of paternity and maternity) cannot be applied without at least one report of a de novo occurrence.
PP1	Not met	No segregation data are available for this variant. No family studies with affected and unaffected members have been reported.
PP2	Not met	The HCI prior score is not available for NTRK1 (gene_not_supported), and no missense constraint Z-score or benign missense depletion data were provided in the evidence packet. Without evidence of a low rate of benign missense variation, PP2 cannot be applied.
PP3	Not met	In silico predictions are mixed and do not provide multiple concordant lines of evidence for a deleterious effect. REVEL score is 0.752 (moderately elevated above 0.5, leaning pathogenic), but BayesDel_noAF score is 0.262 (low, leaning benign). SpliceAI max delta score is 0.16, predicting no significant splice impact. The discordance between REVEL and BayesDel prevents application of PP3, which requires multiple lines of computational evidence agreeing on a deleterious effect.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or clinical data were provided with this case. The variant cannot be matched to a specific clinical presentation without phenotypic information.
PP5	Not met	NM_002529.3:c.1999G>A is absent from ClinVar. No reputable source has classified this variant as pathogenic. PP5 requires a ClinVar entry or equivalent authoritative classification, which does not exist for this variant.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, far below the BA1 threshold of >1% (or >5% per ACMG 2015).	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all population databases. Allele frequency is 0%, far below the BS1 threshold of >0.3% for a rare autosomal recessive disorder expected at very low frequency.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	The variant has not been observed in any individual, healthy or affected, in population databases or published cohorts. No observation in a healthy adult is available to support BS2.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrate a benign effect for p.G667S. No experimental functional data of any kind exist for this specific variant beyond in silico modeling.	PMID:33004339 PMID:33328556
BS4	Not met	No segregation data are available to assess lack of segregation with disease in affected family members.
BP1	Not met	NTRK1-related CIPA (congenital insensitivity to pain with anhidrosis) is caused by both missense and truncating loss-of-function variants. Over 105 NTRK1 mutations have been reported in CIPA, many of which are missense (PMID:30201336). BP1 requires that the gene primarily cause disease through truncating variants, which is not the case for NTRK1.	pvs1_gene_context
BP2	Not met	No phasing or trans-configuration data are available. BP2 requires observation of the variant in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder. Neither configuration has been assessed for this variant.
BP4	Not met	Computational evidence is mixed and does not provide multiple concordant lines suggesting no impact. SpliceAI max delta is 0.16 (predicting no splice effect), but REVEL is 0.752 (elevated, leaning pathogenic), and BayesDel is 0.262 (leaning benign). The discordance among predictors prevents a clear conclusion of no impact. BP4 requires multiple lines of computational evidence to agree on a benign effect.	revel bayesdel spliceai
BP5	Not met	No data are available indicating that the proband has an alternate molecular basis for disease. BP5 requires a co-occurring pathogenic variant in a different gene that fully explains the phenotype.
BP6	Not met	NM_002529.3:c.1999G>A is absent from ClinVar. No reputable source has classified this variant as benign. BP6 requires a ClinVar entry or equivalent authoritative benign classification.	clinvar
BP7	N/A	NM_002529.3:c.1999G>A is a missense variant (p.Gly667Ser), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice impact and low nucleotide conservation.

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