rs11466111

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_002506.3(NGF):​c.239G>C​(p.Arg80Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 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. R80Q) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

NGF
NM_002506.3 missense

Scores

9
8
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.04
Variant links:
Genes affected
NGF (HGNC:7808): (nerve growth factor) This gene is a member of the NGF-beta family and encodes a secreted protein which homodimerizes and is incorporated into a larger complex. This protein has nerve growth stimulating activity and the complex is involved in the regulation of growth and the differentiation of sympathetic and certain sensory neurons. Mutations in this gene have been associated with hereditary sensory and autonomic neuropathy, type 5 (HSAN5), and dysregulation of this gene's expression is associated with allergic rhinitis. [provided by RefSeq, Jul 2008]
NGF-AS1 (HGNC:53922): (NGF antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.818

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NGFNM_002506.3 linkc.239G>C p.Arg80Pro missense_variant Exon 3 of 3 ENST00000369512.3 NP_002497.2 P01138
NGFXM_011541518.3 linkc.404G>C p.Arg135Pro missense_variant Exon 3 of 3 XP_011539820.1 A0A346FYQ1
NGFXM_006710663.4 linkc.239G>C p.Arg80Pro missense_variant Exon 2 of 2 XP_006710726.1 P01138
NGF-AS1NR_157569.1 linkn.207+3317C>G intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NGFENST00000369512.3 linkc.239G>C p.Arg80Pro missense_variant Exon 3 of 3 1 NM_002506.3 ENSP00000358525.2 P01138

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.50
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.070
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.83
D
Eigen
Pathogenic
0.70
Eigen_PC
Uncertain
0.63
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.99
D
M_CAP
Benign
0.073
D
MetaRNN
Pathogenic
0.82
D
MetaSVM
Uncertain
-0.055
T
MutationAssessor
Pathogenic
3.3
M
PrimateAI
Uncertain
0.69
T
PROVEAN
Pathogenic
-5.4
D
REVEL
Uncertain
0.40
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.0070
D
Polyphen
1.0
D
Vest4
0.69
MutPred
0.31
Gain of relative solvent accessibility (P = 0.0098);
MVP
0.67
MPC
1.4
ClinPred
1.0
D
GERP RS
5.1
Varity_R
0.91
gMVP
0.80

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: chr1-115829178; API