13-48463835-G-T

Position:

• chr13-48463835-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PM2 PP5_Moderate

The ENST00000267163.6(RB1):​c.2211G>T​(p.Glu737Asp) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E737K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RB1 ENST00000267163.6 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.27

Genes affected

RB1 (HGNC:9884): (RB transcriptional corepressor 1) The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM1: In a region_of_interest Domain B (size 131) in uniprot entity RB_HUMAN there are 46 pathogenic changes around while only 16 benign (74%) in ENST00000267163.6
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-48463835-G-T is Pathogenic according to our data. Variant chr13-48463835-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 527898.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RB1	NM_000321.3	c.2211G>T	p.Glu737Asp	missense_variant, splice_region_variant	21/27	ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.2211G>T	p.Glu737Asp	missense_variant, splice_region_variant	21/27		NP_001394094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.2211G>T	p.Glu737Asp	missense_variant, splice_region_variant	21/27	1	NM_000321.3	ENSP00000267163.4
RB1	ENST00000650461.1	c.2211G>T	p.Glu737Asp	missense_variant, splice_region_variant	21/27			ENSP00000497193.1
RB1	ENST00000643064.1	c.192+82392G>T		intron_variant				ENSP00000496005.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinoblastoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 17, 2018

For these reasons, this variant has been classified as Pathogenic. Other variants affecting this nucleotide (c.2211G>C and c.2211G>A) have been determined to be pathogenic (PMID: 18181215, 19390654, 22328814, 12541220, 9341870). This suggests that this nucleotide is important for normal RNA splicing, and that other variants at this position may also be pathogenic. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with RB1-related disease, but has been observed to be de novo in an individual affected with bilateral retinoblastoma (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with aspartic acid at codon 737 of the RB1 protein (p.Glu737Asp). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and aspartic acid. This variant also falls at the last nucleotide of exon 21 of the RB1 coding sequence, which is part of the consensus splice site for this exon. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Uncertain	0.098	D
BayesDel_noAF	Benign	-0.10
CADD	Pathogenic	35
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.66	D;.
Eigen	Uncertain	0.19
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.81	T;T
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.32	T;T
MetaSVM	Uncertain	0.11	D
MutationAssessor	Benign	1.1	L;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-1.3	N;.
REVEL	Uncertain	0.38
Sift	Benign	0.041	D;.
Sift4G	Benign	0.16	T;.
Polyphen		0.024	B;.
Vest4		0.29
MutPred		0.51		Gain of catalytic residue at P732 (P = 0.044);Gain of catalytic residue at P732 (P = 0.044);
MVP		0.83
MPC		1.0
ClinPred		0.73	D
GERP RS		6.2
Varity_R		0.70
gMVP		0.51

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.62		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.62		Position offset: 4
DS_DL_spliceai		0.34		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs587776787; hg19: chr13-49037971;