2-211383652-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005235.3(ERBB4):​c.3890C>G​(p.Pro1297Arg) variant causes a missense change involving the alteration of a 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.

Frequency

Genomes: not found (cov: 32)

Consequence

ERBB4
NM_005235.3 missense

Scores

8
8
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 9.37
Variant links:
Genes affected
ERBB4 (HGNC:3432): (erb-b2 receptor tyrosine kinase 4) This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. It encodes a single-pass type I membrane protein with multiple cysteine rich domains, a transmembrane domain, a tyrosine kinase domain, a phosphotidylinositol-3 kinase binding site and a PDZ domain binding motif. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Multiple proteolytic events allow for the release of a cytoplasmic fragment and an extracellular fragment. Mutations in this gene have been associated with cancer. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ERBB4NM_005235.3 linkc.3890C>G p.Pro1297Arg missense_variant Exon 28 of 28 ENST00000342788.9 NP_005226.1 Q15303-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ERBB4ENST00000342788.9 linkc.3890C>G p.Pro1297Arg missense_variant Exon 28 of 28 1 NM_005235.3 ENSP00000342235.4 Q15303-1
ERBB4ENST00000436443.5 linkc.3842C>G p.Pro1281Arg missense_variant Exon 27 of 27 1 ENSP00000403204.1 Q15303-3
ERBB4ENST00000260943.11 linkc.3812C>G p.Pro1271Arg missense_variant Exon 27 of 27 5 ENSP00000260943.7 Q15303-4H3BLT0

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.67
BayesDel_addAF
Pathogenic
0.24
D
BayesDel_noAF
Uncertain
0.10
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.34
T;D;.
Eigen
Pathogenic
0.85
Eigen_PC
Pathogenic
0.85
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.97
D;D;D
M_CAP
Pathogenic
0.31
D
MetaRNN
Uncertain
0.70
D;D;D
MetaSVM
Uncertain
0.44
D
MutationAssessor
Benign
1.9
.;L;.
PrimateAI
Pathogenic
0.81
D
PROVEAN
Uncertain
-2.6
.;D;D
REVEL
Uncertain
0.60
Sift
Pathogenic
0.0
.;D;D
Sift4G
Uncertain
0.012
.;D;D
Polyphen
1.0
.;D;D
Vest4
0.57, 0.57
MutPred
0.24
.;Loss of glycosylation at T1294 (P = 0.0223);.;
MVP
0.83
MPC
1.1
ClinPred
1.0
D
GERP RS
5.4
Varity_R
0.56
gMVP
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: chr2-212248377; API