chr1-17022648-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_003000.3(SDHB):​c.725G>A​(p.Arg242His) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R242C) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )

Consequence

SDHB
NM_003000.3 missense

Scores

17
1
1

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:20

Conservation

PhyloP100: 5.63
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PM1
In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 15 uncertain in NM_003000.3
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr1-17022649-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 186827.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.99
PP5
Variant 1-17022648-C-T is Pathogenic according to our data. Variant chr1-17022648-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 12781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-17022648-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SDHBNM_003000.3 linkuse as main transcriptc.725G>A p.Arg242His missense_variant 7/8 ENST00000375499.8 NP_002991.2 P21912
SDHBNM_001407361.1 linkuse as main transcriptc.671G>A p.Arg224His missense_variant 7/8 NP_001394290.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SDHBENST00000375499.8 linkuse as main transcriptc.725G>A p.Arg242His missense_variant 7/81 NM_003000.3 ENSP00000364649.3 P21912

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152124
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000119
AC:
3
AN:
251440
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135896
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000116
AC:
17
AN:
1461722
Hom.:
0
Cov.:
31
AF XY:
0.00000688
AC XY:
5
AN XY:
727174
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000117
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152124
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000519
AC:
2
ExAC
AF:
0.0000247
AC:
3
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:20
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:5
Pathogenic, criteria provided, single submitterclinical testingGeneDxJan 27, 2023Published functional studies demonstrate a damaging effect: significantly reduced SDH/complex II activity and abrogated SDHAF3 interaction (Kim et al., 2015; Nesti et al., 2015; Dwight et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 12213855, 19393419, 23433498, 25025441, 17102084, 29925701, 34906457, 32782288, 24606901, 22835832, 25736212, 12000816, 25972245, 21173220, 20208144, 22293219, 19258401, 17652212, 19802898, 22270996, 25047027, 19454582, 18551016, 28374168, 25899001, 27573198, 15328326, 24276837, 25873086, 19075037, 16317055, 28503760, 29386252, 29204718, 29951630, 29800631, 29950348, 28748451, 31212687, 30549360, 31104306, 30658386, 28490599, 31492822, 30050099, 26464466, 31589614, 32741965, 33644666, 30787465, 28738844) -
Likely pathogenic, criteria provided, single submitterclinical testingInstitute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU DresdenNov 03, 2021- -
Pathogenic, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMay 01, 2021- -
Pathogenic, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoJun 12, 2013The frequency of this variant in the general population, 0.000012 (3/251440 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. In the published literature, the variant has been reported in multiple individuals affected with PGL-PCC syndrome (PMID: 12000816 (2002), 12213855 (2002), 18551016 (2008), 19351833 (2009), 29386252 (2018), 34439168 (2021), 34906457 (2022)). Functional studies observed decreased stability of the SDHB protein (PMID: 22835832 (2012)) and a severe decrease in succinate dehydrogenase activity (PMID: 25736212 (2015), 25972245 (2015)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesAug 02, 2023The SDHB c.725G>A; p.Arg242His variant (rs74315368) is reported in the literature in individuals affected with paraganglioma or pheochromocytoma (Luiz 2013, Neumann 2002, Neumann 2009, Niemeijer 2017, Young 2002). In at least one family, this variant was observed to segregate with disease (Young 2002). This variant is also reported in ClinVar (Variation ID: 12781). It is only found on three alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.944). Consistent with these predictions, functional assays have observed that this variant exhibits decreased SDH/complex II activity (Kim 2015, Nesti 2015) and increased ubiquitination (Yang 2012). Additionally, other amino acid substitutions at this codon (p.Arg242Cys, p.Arg242Ser) have been reported in individuals with paraganglioma and are considered pathogenic (Badenhop 2004, Neumann 2009). Based on available information, the p.Arg242His variant is considered to be pathogenic. References: Badenhop RF et al. The prevalence of SDHB, SDHC, and SDHD mutations in patients with head and neck paraganglioma and association of mutations with clinical features. J Med Genet. 2004 Jul;41(7):e99. PMID: 15235042. Kim E et al. Structural and functional consequences of succinate dehydrogenase subunit B mutations. Endocr Relat Cancer. 2015 Jun;22(3):387-97. PMID: 25972245. Luiz HV et al. Malignant paraganglioma presenting with hemorrhagic stroke in a child. Pediatrics. 2013 Dec;132(6):e1709-14. PMID: 24276837. Nesti C et al. Additive effect of nuclear and mitochondrial mutations in a patient with mitochondrial encephalomyopathy. Hum Mol Genet. 2015 Jun 1;24(11):3248-56. PMID: 25736212. Neumann HP et al. Clinical predictors for germline mutations in head and neck paraganglioma patients: cost reduction strategy in genetic diagnostic process as fall-out. Cancer Res. 2009 Apr 15;69(8):3650-6. PMID: 19351833. Neumann HP et al. Germ-line mutations in nonsyndromic pheochromocytoma. N Engl J Med. 2002 May 9;346(19):1459-66. PMID: 12000816. Niemeijer ND et al. The phenotype of SDHB germline mutation carriers: a nationwide study. Eur J Endocrinol. 2017 Aug;177(2):115-125. PMID: 28490599. Yang C et al. Missense mutations in the human SDHB gene increase protein degradation without altering intrinsic enzymatic function. FASEB J. 2012 Nov;26(11):4506-16. PMID: 22835832. Young AL et al. Familial malignant catecholamine-secreting paraganglioma with prolonged survival associated with mutation in the succinate dehydrogenase B gene. J Clin Endocrinol Metab. 2002 Sep;87(9):4101-5. PMID: 12213855. -
Paragangliomas 4 Pathogenic:4
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 04, 2011- -
Pathogenic, criteria provided, single submitterclinical testingMGZ Medical Genetics CenterOct 05, 2021- -
Likely pathogenic, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Feb 08, 2024This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 30050099, 32462735, 33362715, 34439168]. This variant is expected to disrupt protein structure [Myriad internal data]. -
Pathogenic, criteria provided, single submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaApr 17, 2019This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PP3. -
Hereditary pheochromocytoma-paraganglioma Pathogenic:4
Pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpApr 27, 2023Variant summary: SDHB c.725G>A (p.Arg242His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251440 control chromosomes. c.725G>A has been reported in the literature in multiple individuals affected with features of Hereditary Paraganglioma-Pheochromocytoma Syndrome (example, Persu_2008, Amar_2007, Young_2002, Benn_2006, Neumann_2004, Neumann_2002). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 12000816, 17652212, 16317055, 15328326, 18551016, 12213855). Ten 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. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria providedresearchSection on Medical Neuroendocrinolgy, National Institutes of Health-- -
Pathogenic, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthAug 08, 2024The c.725G>A variant in the SDHB gene is located on the exon 7 and is predicted to replace arginine with histidine at codon 242 (p.Arg242His). The variant has been reported in multiple unrelated individuals with paraganglioma/pheochromocytoma/renal cell carcinoma (PMID: 12000816, 32661476, 33748650, 36597280, 29925701, 33362715, 34906457). Alternative variants disrupting the same amino acid (p.Arg242Ser, p.Arg242Cys) have been interpreted as pathogenic (ClinVar ID: 239443, 186827). In vitro SDH activity assay and co-immunoprecipitation experiment in mammalian cells demonstrated impaired function and abolished interaction with the SDH aseembly factor SDHAF3 (PMID: 25972245, 28738844). The variant is reported in ClinVar (ID: 12781). The variant is rare in general population according to gnomAD (18/1613846 chromosomes, 0.001%) . Computational prediction algorithms suggest a deleterious impact for this variant (REVEL score 0.94). Therefore, the c.725G>A (p.Arg242His) variant in the SDHB gene is classified as pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingGenetics and Molecular Pathology, SA PathologyNov 10, 2020The SDHB c.725G>A variant is a single nucleotide substitution from a guanine to an adenonine at position 725 which is predicted to change the arginine at position 242 in the protein to histidine. The variant has been reported multiple times in the literature in association with disease (PMID: 12000816, 12213855, 15328326, 28490599) (PS1). Functional studies demonstrate that the variant has a detrimental effect on protein function (PMID: 25972245, 22835832) (PS3). The variant is listed in dbSNP (rs74315368) and is rare in population databases (gnomAD 3 het/251,440 total, 0 hom). The variant is described in ClinVar as pathogenic (ClinVar ID: 27820) and HGMD (2020.3) as disease causing (PP5). Computational predictions support a deleterious effect on the gene or gene product. -
Gastrointestinal stromal tumor Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 04, 2011- -
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsAug 20, 2021- -
Hereditary cancer-predisposing syndrome Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsNov 08, 2022The p.R242H pathogenic mutation (also known as c.725G>A), located in coding exon 7 of the SDHB gene, results from a G to A substitution at nucleotide position 725. The arginine at codon 242 is replaced by histidine, an amino acid with highly similar properties. The p.R242H mutation has been well described in published literature. It has been identified in numerous individuals with tumors across the paraganglioma-pheochromocytoma (PGL-PCC) syndrome spectrum, including thoracic, pelvic, and head and neck PGL, adrenal PCC, and renal cell carcinoma (Neumann HP et al. JAMA. 2004 Aug;292:943-51; Ghayee HK et al. Endocr. Relat. Cancer. 2009 Mar;16:291-9; Luiz HV et al. Pediatrics. 2013 Dec;32:e1709-14; Persu A et al. J. Hypertens. 2008 Jul;26:1395-401; Burnichon N et al. J. Clin. Endocrinol. Metab. 2009 Aug;94:2817-27; Merlo A et al. J. Clin. Endocrinol. Metab 2013 Oct;98:E1661-6; Rattenberry E et al. J. Clin. Endocrinol. Metab. 2013 Jul;98:E1248-56; van Hulsteijn LT et al. Fam. Cancer. 2014 Dec;13:651-7; Janssen I et al. Clin. Cancer Res. 2015 Sep;21:3888-95; Gill AJ et al. Am. J. Surg. Pathol. 2014 Dec;38:1588-602). In one study, mutant yeast strains with this mutation showed a significant defect and structural analysis suggested that this mutation alters the conformation of the protein, causing a decrease in the positive surface extent of the mutant protein (Nesti C et al. Hum. Mol. Genet. 2015 Jun;24:3248-56). Additionally, structural modeling of this mutation has predicted disruption of the electron path and impaired functional activity (Kim E et al. Endocr. Relat. Cancer. 2015 Jun;22:387-97). Of note, two different alterations at the same codon, p.R242C and p.R242S, have also been reported in patients with head/neck PGLs and PCCs (Panizza E et al. Hum. Mol. Genet. 2013 Feb;22:804-15; Neumann HP et al. Cancer Res. 2009 Apr;69:3650-6; Lefebvre S et al. Horm. Metab. Res. 2012 May;44:334-8; Badenhop RF et al. J. Med. Genet. 2004 Jul;41:e99). Based on the available evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submittercurationSema4, Sema4Jul 06, 2021- -
Mitochondrial complex 2 deficiency, nuclear type 4 Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingVictorian Clinical Genetics Services, Murdoch Childrens Research InstituteFeb 02, 2022Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with mitochondrial complex II deficiency, nuclear type 4 (MIM#619224), pheochromocytoma (MIM#171300) and paragangliomas 4 (MIM#115310). (I) 0108 - This gene is associated with both recessive and dominant disease. However, the genotype-phenotype correlation is currently unestablished (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance (GeneReviews). I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to histidine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (3 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated 4Fe-4S dicluster domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in several individuals with pheochromocytoma (MIM#171300) and/or paragangliomas 4 (MIM#115310), rarely in non-paraganglioma tumours such as gastrointestinal stromal tumour and a single case of mitochondrial encephalomyopathy (PMID: 32460727, 33748650, 28490599, 21173220, 25736212). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pheochromocytoma;C0238198:Gastrointestinal stromal tumor;C1861848:Paragangliomas 4 Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 21, 2024This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 242 of the SDHB protein (p.Arg242His). This variant is present in population databases (rs74315368, gnomAD 0.007%). This missense change has been observed in individuals with sporadic and familial hereditary paragangliomas and/or pheochromocytomas (PMID: 12000816, 12213855, 17102084, 20208144, 21173220, 22270996, 24276837, 25736212). ClinVar contains an entry for this variant (Variation ID: 12781). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SDHB protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects SDHB function (PMID: 22835832, 25736212, 25972245). This variant disrupts the p.Arg242 amino acid residue in SDHB. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). 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. -
SDHB-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingDASAFeb 14, 2022Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 25972245; 25736212; 22835832) - PS3. The c.725G>A;p.(Arg242His) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 12781; OMIM: 185470.0004; PMID: 12000816; 20208144; 24276837; 12213855; 17102084; 22270996) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (Fer4) - PM1. This variant is not present in population databases (rs7431536, gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. Pathogenic missense variant in this residue have been reported (ClinVar ID: 239443 - c.724C>A (p.Arg242Ser); ClinVar ID: 186827 - c.724C>T (p.Arg242Cys)) - PM5. Missense variant in SDHB that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease - PP2. In summary, the currently available evidence indicates that the variant is pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.84
BayesDel_addAF
Pathogenic
0.43
D
BayesDel_noAF
Pathogenic
0.56
CADD
Pathogenic
33
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.86
D
Eigen
Pathogenic
0.96
Eigen_PC
Pathogenic
0.91
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Pathogenic
0.99
D
M_CAP
Pathogenic
0.69
D
MetaRNN
Pathogenic
0.99
D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
3.5
M
PrimateAI
Pathogenic
0.80
T
PROVEAN
Uncertain
-4.0
D
REVEL
Pathogenic
0.94
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.93
MutPred
0.94
Loss of MoRF binding (P = 0.0969);
MVP
0.99
MPC
0.78
ClinPred
1.0
D
GERP RS
5.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.78
gMVP
0.89

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs74315368; hg19: chr1-17349143; API