1-156873723-G-C

Position:

• chr1-156873723-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1 PM2

The ENST00000524377.7(NTRK1):​c.941G>C​(p.Arg314Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R314C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: NTRK1 ENST00000524377.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

NTRK1 (HGNC:8031): (neurotrophic receptor tyrosine kinase 1) This gene encodes a member of the neurotrophic tyrosine kinase receptor (NTKR) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. The presence of this kinase leads to cell differentiation and may play a role in specifying sensory neuron subtypes. Mutations in this gene have been associated with congenital insensitivity to pain, anhidrosis, self-mutilating behavior, cognitive disability and cancer. Alternate transcriptional splice variants of this gene have been found, but only three have been characterized to date. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a domain Ig-like C2-type 2 (size 66) in uniprot entity NTRK1_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in ENST00000524377.7
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTRK1	NM_002529.4	c.941G>C	p.Arg314Pro	missense_variant	8/17	ENST00000524377.7	NP_002520.2
NTRK1	NM_001012331.2	c.941G>C	p.Arg314Pro	missense_variant	8/16		NP_001012331.1
NTRK1	NM_001007792.1	c.851G>C	p.Arg284Pro	missense_variant	9/17		NP_001007793.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTRK1	ENST00000524377.7	c.941G>C	p.Arg314Pro	missense_variant	8/17	1	NM_002529.4	ENSP00000431418	P4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Benign	-0.048	T
BayesDel_noAF	Benign	-0.31
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.60	.;.;D;T
Eigen	Benign	-0.0076
Eigen_PC	Benign	-0.024
FATHMM_MKL	Benign	0.25	N
LIST_S2	Uncertain	0.90	D;D;D;D
M_CAP	Benign	0.018	T
MetaRNN	Uncertain	0.56	D;D;D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.1	.;M;M;.
MutationTaster	Benign	0.71	N;N;N;N
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-2.5	D;D;D;D
REVEL	Benign	0.21
Sift	Benign	0.062	T;T;T;T
Sift4G	Benign	0.21	T;T;T;T
Polyphen		0.93, 0.62	.;P;P;.
Vest4		0.69
MutPred		0.59		.;Gain of catalytic residue at W315 (P = 0.0151);Gain of catalytic residue at W315 (P = 0.0151);Gain of catalytic residue at W315 (P = 0.0151);
MVP		0.65
MPC		0.87
ClinPred		0.92	D
GERP RS		3.0
Varity_R		0.74
gMVP		0.97

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-156843515;