rs786201161

chr1-17024076-T-C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Moderate PM2 PP3_Strong PP5_Very_Strong

The NM_003000.3(SDHB):c.541-2A>G variant causes a splice acceptor change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SDHB NM_003000.3 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 6.92

Genes affected

SDHB (HGNC:10681): (succinate dehydrogenase complex iron sulfur subunit B) This tumor suppressor gene encodes the iron-sulfur protein subunit of the succinate dehydrogenase (SDH) enzyme complex which plays a critical role in mitochondria. The SDH enzyme complex is composed of four nuclear-encoded subunits. This enzyme complex converts succinate to fumarate which releases electrons as part of the citric acid cycle, and the enzyme complex additionally provides an attachment site for released electrons to be transferred to the oxidative phosphorylation pathway. The SDH enzyme complex plays a role in oxygen-related gene regulation through its conversion of succinate, which is an oxygen sensor that stabilizes the hypoxia-inducible factor 1 (HIF1) transcription factor. Sporadic and familial mutations in this gene result in paragangliomas, pheochromocytoma, and gastrointestinal stromal tumors, supporting a link between mitochondrial dysfunction and tumorigenesis. Mutations in this gene are also implicated in nuclear type 4 mitochondrial complex II deficiency. [provided by RefSeq, Jun 2022]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.0599051 fraction of the gene. Cryptic splice site detected, with MaxEntScore 6.7, offset of 38, new splice context is: attctctgtgcctgctgtAGcac. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 1-17024076-T-C is Pathogenic according to our data. Variant chr1-17024076-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 183925.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-17024076-T-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDHB	NM_003000.3	c.541-2A>G		splice_acceptor_variant		ENST00000375499.8
SDHB	NM_001407361.1	c.487-2A>G		splice_acceptor_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDHB	ENST00000375499.8	c.541-2A>G		splice_acceptor_variant		1	NM_003000.3	P1
SDHB	ENST00000463045.3	c.370-2A>G		splice_acceptor_variant		3
SDHB	ENST00000491274.6	c.499-2A>G		splice_acceptor_variant		5
SDHB	ENST00000485515.5	n.475-2A>G		splice_acceptor_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary pheochromocytoma-paraganglioma Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 07, 2021	Variant summary: SDHB c.541-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes a 3 prime acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 249478 control chromosomes. c.541-2A>G has been reported in the literature in individuals affected with Hereditary Paraganglioma-Pheochromocytoma Syndrome with reduced penetrance (e.g. Timmers_2007, Neumann_2009, Jochmanova_2017). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	research	Section on Medical Neuroendocrinolgy, National Institutes of Health	-	- -

SDHB-Related Disorders Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

The c.541-2A>G variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. The variant has been reported in three studies in which it is found in a total of four hereditary paraganglioma-pheochromocytoma syndrome patients, all in a heterozygous state (Timmers et al. 2007; Ricketts et al. 2012; Choat et al. 2014). The variant was absent from an unaffected brother of one of the patients (Choat et al. 2014). Control data are unavailable for this variant which is not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium. Based on the evidence and the potential impact of splice acceptor variants, the c.541-2A>G variant is classified as likely pathogenic for SDHB-related disorders. -

Pheochromocytoma;C0238198:Gastrointestinal stromal tumor;C1861848:Paragangliomas 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 20, 2024

This sequence change affects an acceptor splice site in intron 5 of the SDHB gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SDHB are known to be pathogenic (PMID: 19454582, 19802898). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with leukodystrophic encephalopathy and paragangliomas and pheochromocytomas (PMID: 17200167, 23083876, 25298897, 26642834). This variant is also known as IVS5–2A>G. ClinVar contains an entry for this variant (Variation ID: 183925). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Paragangliomas 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Feb 08, 2024

This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 31705439, 25298897, 17538171, 29504908, 23083876]. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Dec 21, 2022

Canonical splice site variant predicted to result in an in-frame deletion of a critical region, including the 4FE-4S ferredoxin-type domain and Iron-sulfur 2 (4Fe-4S), Iron-sulfur 3 (3Fe-4S), and ubiquinone binding sites (UniProt); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23083876, 25525159, 25298897, 28748451, 25873086, 17200167, 28374168, 27159321, 28973655, 30352407, 19351833, 26642834, 29504908, 25371406, 31705439, 31579262, 32124427, 31492822, 27535533, 34703596) -

Gastrointestinal stromal tumor Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Apr 25, 2022

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 07, 2022

The c.541-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 6 in the SDHB gene. This mutation was detected in several individuals with personal and/or family history of pheochromocytoma, paraganglioma, and renal cell carcinoma (Ambry internal data; Timmers HJ et al. J Clin Endocrinol Metab. 2007;92(3):779-86. Ricketts CJ et al. J Urol. 2012 Dec;188(6):2063-71. Choat H, et al. Case Rep Endocrinol 2014 ; 2014:502734; Casey RT et al. J. Clin. Endocrinol. Metab., 2017 11;102:4013-4022; Huang Y et al. Endocr Connect, 2018 Dec;7:1217-1225). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). As such, this alteration is classified as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.32
Cadd	Pathogenic	27
Dann	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.92
FATHMM_MKL	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.99		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs786201161; hg19: chr1-17350571; COSMIC: COSV64964901; COSMIC: COSV64964901;