rs587781270

Variant names:

• chr1-17033058-A-T
• rs587781270
• NM_003000.3:c.286+2T>A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_003000.3(SDHB):​c.286+2T>A variant causes a splice donor, intron 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SDHB NM_003000.3 splice_donor, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 8.19

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 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-17033058-A-T is Pathogenic according to our data. Variant chr1-17033058-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 140773.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDHB	NM_003000.3	c.286+2T>A		splice_donor_variant, intron_variant	Intron 3 of 7	ENST00000375499.8	NP_002991.2
SDHB	NM_001407361.1	c.286+2T>A		splice_donor_variant, intron_variant	Intron 3 of 7		NP_001394290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDHB	ENST00000375499.8	c.286+2T>A		splice_donor_variant, intron_variant	Intron 3 of 7	1	NM_003000.3	ENSP00000364649.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Paragangliomas 4 Pathogenic:2

Feb 08, 2024

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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: 28409892, 30201732, 30877234, 28374168]. -

Nov 01, 2016

Center for Human Genetics, Inc, Center for Human Genetics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:2

Jan 04, 2022

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP4, PM2, PS4_moderate, PVS1 -

Jul 02, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with SDHB-related tumors (PMID: 16912137, 19075037, 23083876, 30877234, 31492822, 32741965); This variant is associated with the following publications: (PMID: 25525159, 32741965, 23083876, 28152038, 31492822, 28409892, 16912137, 31579262, 19075037, 30787465, 30877234, 35668420) -

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

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 3 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 malignant paraganglioma and renal cell carcinoma (PMID: 16199547, 16912137, 19454582, 19802898, 23083876). ClinVar contains an entry for this variant (Variation ID: 140773). 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. -

Gastrointestinal stromal tumor Pathogenic:1

Mar 15, 2022

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

May 07, 2021

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.286+2T>A intronic pathogenic mutation results from a T to A substitution two nucleotides after coding exon 3 in the SDHB gene. This mutation has been detected in an individual with a malignant paraganglioma (PGL) (Brouwers FM et al. J. Clin. Endocrinol. Metab. 2006 Nov;91:4505-9), a 35 year old individual with a malignant pheochromocytoma (Ben Aim L et al. J Med Genet, 2019 08;56:513-520), a 37 year old male diagnosed with renal cell carcinoma (Ricketts CJ et al. J. Urol. 2012 Dec;188:2063-71), and in an 18 year old male who was diagnosed with a PGL whose father reportedly had a head and neck PGL (Ghayee HK et al. Endocr. Relat. Cancer. 2009 Mar;16:291-9). This alteration was also identified in a cohort of 950 pheochromocytoma-paraganglioma syndrome (PPGL) and head and neck paraganglioma (HNPGL) patients (Bayley JP et al. J Med Genet, 2020 02;57:96-103). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

SDHB-related disorder Pathogenic:1

Aug 16, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The SDHB c.286+2T>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant was reported in individuals with SDHB-related tumors, including malignant paraganglioma (Brouwers et al. 2006. PubMed ID: 16912137; Ghayee et al. 2008. PubMed ID: 19075037), renal cell carcinoma (Ricketts et al. 2012. PubMed ID: 23083876), pheochromocytoma (Ben Aim et al. 2019. PubMed ID: 30877234), and a carotid body tumor (Greenberg et al. 2020. PubMed ID: 32741965). This variant has not been reported in a large population database, indicating this variant is rare. It is reported in ClinVar as pathogenic by multiple laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/140773/). Variants that disrupt the consensus splice donor site in SDHB are expected to be pathogenic. This variant is interpreted as pathogenic. -

Hereditary pheochromocytoma-paraganglioma Pathogenic:1

-

Section on Medical Neuroendocrinolgy, National Institutes of Health

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.14
CADD	Pathogenic	32
DANN	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.87
FATHMM_MKL	Pathogenic	1.0	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.94		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.94		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: rs587781270; hg19: chr1-17359553;