NM_004168.4:c.91C>T
Variant summary
Our verdict is Likely pathogenic. The variant received 8 ACMG points: 9P and 1B. PVS1PP5BS1_Supporting
The NM_004168.4(SDHA):c.91C>T(p.Arg31*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,613,500 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004168.4 stop_gained
Scores
Clinical Significance
Conservation
Publications
- hereditary pheochromocytoma-paragangliomaInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- pheochromocytoma/paraganglioma syndrome 5Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- mitochondrial complex II deficiency, nuclear type 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- neurodegeneration with ataxia and late-onset optic atrophyInheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- Leigh syndromeInheritance: AR Classification: MODERATE Submitted by: Ambry Genetics, ClinGen
- familial isolated dilated cardiomyopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- gastrointestinal stromal tumorInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Leigh syndrome with leukodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- mitochondrial complex II deficiencyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- dilated cardiomyopathy 1GGInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_pathogenic. The variant received 8 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SDHA | NM_004168.4 | c.91C>T | p.Arg31* | stop_gained | Exon 2 of 15 | ENST00000264932.11 | NP_004159.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SDHA | ENST00000264932.11 | c.91C>T | p.Arg31* | stop_gained | Exon 2 of 15 | 1 | NM_004168.4 | ENSP00000264932.6 | ||
| ENSG00000286001 | ENST00000651543.1 | n.91C>T | non_coding_transcript_exon_variant | Exon 2 of 24 | ENSP00000499215.1 |
Frequencies
GnomAD3 genomes 0.000243 AC: 37AN: 152202Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000195 AC: 49AN: 251180 AF XY: 0.000228 show subpopulations
GnomAD4 exome AF: 0.000420 AC: 614AN: 1461298Hom.: 0 Cov.: 30 AF XY: 0.000440 AC XY: 320AN XY: 727008 show subpopulations
Age Distribution
GnomAD4 genome 0.000243 AC: 37AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.000256 AC XY: 19AN XY: 74356 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Pathogenic:15
PP1, PP4, PVS1 -
SDHA: PVS1, PP1:Strong -
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This nonsense variant causes the premature termination of SDHA protein synthesis. In the published literature, the variant has been reported in patients with paragangliomas, pheochromocytomas, and gastrointestinal stromal tumors (PMIDs: 26173966 (2016), 26490314 (2016), 25494863 (2015), 26259135 (2015), 23666964 (2013), 22955521 (2013), 23174939 (2013)). Based on the available information, this variant is classified as pathogenic. -
The SDHA c.91C>T; p.Arg31Ter variant (rs142441643) is reported in the literature associated with disease in multiple patients. Genetic testing of a gastrointestinal stromal tumor (GIST) in a young adult patient identified the p.Arg31Ter variant in trans from another pathogenic variant (p.Arg589Trp); subsequent testing revealed that the p.Arg31Ter variant was germline whereas the p.Arg589Trp variant was detected only in the tumor (Pantaleo 2011). Another study of paragangliomas (PGL) and pheochromocytomas identified the p.Arg31Ter variant in four tumors (patients were heterozygous for germline p.Arg31Ter, whereas tumors showed loss-of-heterozygosity); however, the same variant was also identified in 0.3% of healthy controls (Korpershoek 2011). A number of other studies have reported the p.Arg31Ter variant in both PGL and non-PGL tumors, often with evidence of p.Arg31Ter as a germline variant in affected patients (Boikos 2016, Denes 2015, Else 2017, Lussey-Lepoutre 2016, Niemeijer 2015, Oudijk 2013, Rattenberry 2013, Wagner 2013). Finally, p.Arg31Ter was also identified in trans from a germline p.Cys189Gly variant in a patient with multisystem mitochondrial disease (Renkema 2015). The p.Arg31Ter variant is classified as pathogenic by multiple laboratories in ClinVar (Variation ID: 142601). It is found in the general population databases with an overall allele frequency of 0.02% (58/276948 alleles) in the Genome Aggregation Database. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. However, pathogenic heterozygous SDHA variants have incomplete penetrance (Casey 2017) and the individual risk has yet to be determined. References: Boikos SA et al. Carney triad can be (rarely) associated with germline succinate dehydrogenase defects. Eur J Hum Genet. 2016 Apr;24(4):569-73. Casey RT et al. SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity. Mol Genet Genomic Med. 2017 Mar 2;5(3):237-250. Denes J et al. Heterogeneous genetic background of the association of pheochromocytoma/paraganglioma and pituitary adenoma: results from a large patient cohort. J Clin Endocrinol Metab. 2015 Mar;100(3):E531-41. Else T et al. Adrenocortical carcinoma and succinate dehydrogenase gene mutations: an observational case series. Eur J Endocrinol. 2017 Nov;177(5):439-444. Korpershoek E et al. SDHA immunohistochemistry detects germline SDHA gene mutations in apparently sporadic paragangliomas and pheochromocytomas. J Clin Endocrinol Metab. 2011 Sep;96(9):E1472-6. Lussey-Lepoutre C et al. In Vivo Detection of Succinate by Magnetic Resonance Spectroscopy as a Hallmark of SDHx Mutations in Paraganglioma. Clin Cancer Res. 2016 Mar 1;22(5):1120-9. Niemeijer ND et al. Succinate Dehydrogenase (SDH)-Deficient Pancreatic Neuroendocrine Tumor Expands the SDH-Related Tumor Spectrum. J Clin Endocrinol Metab. 2015 Oct;100(10):E1386-93. Oudijk L et al. SDHA mutations in adult and pediatric wild-type gastrointestinal stromal tumors. Mod Pathol. 2013 Mar;26(3):456-63. Pantaleo MA et al. SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst. 2011 Jun 22;103(12):983-7. Rattenberry E et al. A comprehensive next generation sequencing-based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma. J Clin Endocrinol Metab. 2013 Jul;98(7):E1248-56. Renkema GH et al. SDHA mutations causing a multisystem mitochondrial disease: novel mutations and genetic overlap with hereditary tumors. Eur J Hum Genet. 2015 Feb;23(2):202-9. Wagner AJ et al. Loss of expression of SDHA predicts SDHA mutations in gastrointestinal stromal tumors. Mod Pathol. 2013 Feb;26(2):289-94. -
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Observed with a second SDHA variant on the opposite allele (in trans) in an individual with Leigh syndrome (Renkema 2015); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate loss of protein expression (Dubard Gault 2018); This variant is associated with the following publications: (PMID: 31368675, 30854332, 25394176, 27171833, 23252569, 27604842, 28546994, 22974104, 30877234, 25525159, 24886695, 23612575, 25494863, 26259135, 23109135, 21505157, 23666964, 21752896, 27895137, 28819017, 22955521, 23174939, 30068732, 29978187, 26173966, 29625052, 26689913, 29177515, 28500238, 31169996, 29978154, 32581362, 31827275, 34308366, 31589614, 33372952, 33077847, 33960148, 33674644, 24781757) -
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Pheochromocytoma/paraganglioma syndrome 5 Pathogenic:12
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The SDHA c.91C>T variant is classified as Pathogenic (PVS1, PS4_Moderate, PS3) The SDHA c.91C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 31 (PVS1). This variant has been reported in multiple individuals with gastrointestinal stromal tumors (GIST), paragangliomas (PGL), pheochromocytomas (PCC), Carney triad (PMID: 26173966), as well as non-PGL tumors (PMID: 21505157, 22955521, 23174939, 21752896, 23666964, 25494863, 26259135) (PS4_Moderate). Well-established functional studies show a deleterious effect of this variant (PMID:24781757) (PS3). The variant has been reported in dbSNP (rs142441643) and has been reported in population databases (gnomAD 37/152202, 0 homozygotes). The variant has been reported in the HGMD database as disease causing (CM114717) and as Pathogenic/Likely pathogenic by other diagnostic laboratories (ClinVar Variation ID: 142601). -
Based 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 SDHA-related disorders (MIM#613642, MIM#252011, MIM#619259, MIM#614165). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance. Variants in this gene are known to have reduced penetrance for paragangliomas 5 (PMID: 29978154). (I) 0204 - Variant is predicted to result in a truncated protein (premature termination codon is located within the first 102 nucleotides of the coding sequence and is predicted to escape nonsense-mediated decay). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2: 59 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported multiple times in association with paraganglioma. In addition, it has also been reported in compound heterozygous state in an individual with Leigh syndrome (ClinVar, PMID: 24781757). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Functional studies showed a partial reduction in protein and almost complete loss of complex II activity (PMID: 24781757). (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -
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This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -
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Criteria applied: PVS1,PS3_SUP,PS4_MOD -
This 6 year old male with global developmental delays (at-risk for mild intellectual disability), ADHD, disruptive behavior, and mild overgrowth was found to carry a paternally inherited nonsense variant in the SDHA gene. The R31X pathogenic variant in the SDHA gene has been reported previously in the heterozygous state in association with hereditary paraganglioma-pheochromocytoma syndrome (Korpershoek et al., 2011; Rattenberry et al., 2013; Batsis et al., 2016) and in individuals with gastrointestinal stromal tumors (Pantaleo et al., 2011; Wagner et al., 2013; Oudijk et al., 2013). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The patient does not yet show any signs of hereditary paraganglioma-pheochromocytoma syndrome. His father has not yet been formally evaluated, but he reports a history of hypertension. -
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This mutation was observed in 9 patients in our cancer study. Additional supporting evidence for this mutation contributing to the specific cancers manifested by patients in our cohort, were in the settings of GIST and neuroblastoma. For patients with other cancer types in our cohort, this alteration is suggestive of an independent risk factor for cancers than experienced by the patients. -
Dilated cardiomyopathy 1GG;C3279992:Pheochromocytoma/paraganglioma syndrome 5;C5543254:Neurodegeneration with ataxia and late-onset optic atrophy;C5700310:Mitochondrial complex II deficiency, nuclear type 1 Pathogenic:2
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Hereditary cancer-predisposing syndrome Pathogenic:2
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The p.R31* pathogenic mutation (also known as c.91C>T), located in coding exon 2 of the SDHA gene, results from a C to T substitution at nucleotide position 91. This changes the amino acid from an arginine to a stop codon within coding exon 2. This mutation has been reported in multiple individuals diagnosed with isolated paraganglioma (Rattenberry E et al. J. Clin. Endocrinol. Metab. 2013 Jul;98:E1248-56; Bahougne T et al. Endocr. Relat. Cancer. 2017 Feb;24:L7-L11; Lussey-Lepoutre C et al. Clin. Cancer Res. 2016 Mar;22:1120-9). This mutation was also detected in 2/692 (0.3%) Dutch controls, which suggests a low penetrance of paragangliomas in individuals with this mutation (Korpershoek E et al. J. Clin. Endocrinol. Metab. 2011 Sep;96:E1472-6). This alteration has also been reported in individuals with gastrointestinal stromal tumors and pheochromocytomas, an individual with adrenocortical carcinoma, and an individual with SDHA-deficient renal cell carcinoma (Pantaleo MA et al. J. Natl. Cancer Inst. 2011 Jun;103:983-7; Wagner AJ et al. Mod. Pathol. 2013 Feb;26:289-94; Oudijk L et al. Mod. Pathol. 2013 Mar;26:456-63; Else T et al. Eur. J. Endocrinol. 2017 Nov;177:439-444; McEvoy CR et al. NPJ Precis Oncol. 2018 Mar;2:9; Dubard Gault M et al. Cold Spring Harb Mol Case Stud. 2018 08;4:(4); Tufton N et al. Endocr. Relat. Cancer. 2017 07;24:L43-L49). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -
SDHA-related disorder Pathogenic:2
The SDHA c.91C>T variant is predicted to result in premature protein termination (p.Arg31*). This variant has been reported in individuals with paragangliomas/pheochromocytomas, gastrointestinal stromal tumors, and pulmonary chondromas (Pantaleo et al. 2011. PubMed ID: 21505157; Korpershoek et al. 2011. PubMed ID: 21752896; Wagner et al. 2013. PubMed ID: 22955521; Boikos et al. 2016. PubMed ID: 26173966). Note that penetrance for this disorder is incomplete (see, for example, Else et al. 2018. PubMed ID: 20301715). This variant is reported in 0.041% of alleles in individuals of European (Non-Finnish) descent in gnomAD. In ClinVar, this variant has been reported as pathogenic by several clinical laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/142601/). In summary, we interpret this variant as pathogenic for autosomal dominant paragangliomas (OMIM #614165). -
This nonsense variant found in exon 2 of 15 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been reported in multiple individuals with gastrointestinal stromal tumors (GIST), paragangliomas (PGL), pheochromocytomas (PCC), Carney triad (PMID: 26173966), and non-PGL tumors (PMID: 21505157, 22955521, 23174939, 21752896, 23666964, 25494863, 26259135). This variant has also been reported as a compound heterozygous change in an individual diagnosed with autosomal-recessive complex II deficiency (PMID: 24781757). Functional studies showed that the presence of this variant caused reduced expression of SDHA protein and mitochondrial complex II enzyme activity (PMID: 24781757). Loss-of-function variants are an established mechanism of disease in SDHA-related disorders (HGMD, ClinVar database). The c.91C>T (p.Arg31Ter) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.021% (59/282590) and thus is presumed to be rare. Based on the available evidence, the c.91C>T (p.Arg31Ter) variant is classified as Pathogenic. -
Pheochromocytoma/paraganglioma syndrome 5;C5700310:Mitochondrial complex II deficiency, nuclear type 1 Pathogenic:1Other:1
This sequence change creates a premature translational stop signal (p.Arg31*) in the SDHA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SDHA are known to be pathogenic (PMID: 22974104, 24781757). This variant is present in population databases (rs142441643, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with gastrointestinal stromal tumors (GIST), paragangliomas (PGL), pheochromocytomas (PCC), Carney triad and autosomal-recessive complex II deficiency (PMID: 21505157, 21752896, 22955521, 23174939, 23666964, 24781757, 25494863, 26173966, 26259135). ClinVar contains an entry for this variant (Variation ID: 142601). For these reasons, this variant has been classified as Pathogenic. -
Variant interpreted as Pathogenic and reported on 04-20-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Mitochondrial complex II deficiency, nuclear type 1 Pathogenic:1
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Leigh syndrome Pathogenic:1
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PP4,PP5. -
Carney triad Pathogenic:1
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Rhabdomyosarcoma Pathogenic:1
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Pilocytic astrocytoma Pathogenic:1
This is a nonsense alteration in which a C is replaced by a T at coding nucleotide 91 and is predicted to change an Arginine to a premature stop codon at amino acid codon 31. Classification criteria: PVS1, PS1, PP5. -
Gastrointestinal stromal tumor Pathogenic:1
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Dilated cardiomyopathy 1GG Pathogenic:1
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Neurodegeneration with ataxia and late-onset optic atrophy Pathogenic:1
Variant summary: SDHA c.91C>T (p.Arg31X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Variants downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 0.0002 in 251180 control chromosomes (gnomAD). c.91C>T has been reported in the literature in multiple individuals affected with pheochromocytomas and paragangliomas, SSDH-deficient gastrointestinal stromal tumors and significant ataxia, with progressive cerebellar atrophy (examples: Korpershoek_ 2011, Panteleo_ 2022, Sturrock_ 2020). 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: 35059314, 21752896, 33960148). Twenty two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic (n=20)/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. -
Intellectual disability Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at