4-2831573-G-C

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate

The NM_001122681.2(SH3BP2):​c.1244G>C​(p.Arg415Pro) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SH3BP2
NM_001122681.2 missense, splice_region

Scores

8
8
2

Clinical Significance

Pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 7.78
Variant links:
Genes affected
SH3BP2 (HGNC:10825): (SH3 domain binding protein 2) The protein encoded by this gene has an N-terminal pleckstrin homology (PH) domain, an SH3-binding proline-rich region, and a C-terminal SH2 domain. The protein binds to the SH3 domains of several proteins including the ABL1 and SYK protein tyrosine kinases , and functions as a cytoplasmic adaptor protein to positively regulate transcriptional activity in T, natural killer (NK), and basophilic cells. Mutations in this gene result in cherubism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.96
PP5
Variant 4-2831573-G-C is Pathogenic according to our data. Variant chr4-2831573-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 7550.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SH3BP2NM_001122681.2 linkc.1244G>C p.Arg415Pro missense_variant, splice_region_variant 9/13 ENST00000503393.8 NP_001116153.1 P78314-1A0A384N6E5
SH3BP2NM_001145856.2 linkc.1415G>C p.Arg472Pro missense_variant, splice_region_variant 9/13 NP_001139328.1 P78314-4
SH3BP2NM_001145855.2 linkc.1328G>C p.Arg443Pro missense_variant, splice_region_variant 9/13 NP_001139327.1 P78314-3
SH3BP2NM_003023.4 linkc.1244G>C p.Arg415Pro missense_variant, splice_region_variant 9/13 NP_003014.3 P78314-1A0A384N6E5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SH3BP2ENST00000503393.8 linkc.1244G>C p.Arg415Pro missense_variant, splice_region_variant 9/131 NM_001122681.2 ENSP00000422168.3 P78314-1

Frequencies

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

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Fibrous dysplasia of jaw Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 01, 2001- -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 16, 2024This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 415 of the SH3BP2 protein (p.Arg415Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with cherubism (PMID: 11381256, 19576004, 28721660). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 7550). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SH3BP2 function (PMID: 22153077). This variant disrupts the p.Arg415 amino acid residue in SH3BP2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11381256, 21045962, 22795151, 24382142, 24608212, 26064398, 28644570; 30236129)). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Pathogenic
0.54
D
BayesDel_noAF
Pathogenic
0.54
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.52
D;.;D;D;.;D
Eigen
Uncertain
0.59
Eigen_PC
Uncertain
0.55
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.90
.;D;.;.;D;D
M_CAP
Pathogenic
0.31
D
MetaRNN
Pathogenic
0.96
D;D;D;D;D;D
MetaSVM
Pathogenic
1.0
D
PrimateAI
Uncertain
0.66
T
PROVEAN
Uncertain
-2.9
D;D;D;D;D;D
REVEL
Pathogenic
0.84
Sift
Uncertain
0.0060
D;D;D;D;D;D
Sift4G
Benign
0.34
T;T;T;T;T;T
Polyphen
0.99
D;.;D;D;.;D
Vest4
0.71
MutPred
0.84
Gain of glycosylation at R415 (P = 0.0237);.;Gain of glycosylation at R415 (P = 0.0237);Gain of glycosylation at R415 (P = 0.0237);.;Gain of glycosylation at R415 (P = 0.0237);
MVP
0.97
MPC
0.79
ClinPred
0.96
D
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.98

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs121909149; hg19: chr4-2833300; API