1-17053998-AG-A

Position:

• chr1-17053998-AG-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The ENST00000375499.8(SDHB):​c.21del​(p.Ser8ProfsTer2) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. L7L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SDHB ENST00000375499.8 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 3.67

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 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 300 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-17053998-AG-A is Pathogenic according to our data. Variant chr1-17053998-AG-A is described in ClinVar as [Pathogenic]. Clinvar id is 480807.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-17053998-AG-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDHB	NM_003000.3	c.21del	p.Ser8ProfsTer2	frameshift_variant	1/8	ENST00000375499.8	NP_002991.2
SDHB	NM_001407361.1	c.21del	p.Ser8ProfsTer2	frameshift_variant	1/8		NP_001394290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDHB	ENST00000375499.8	c.21del	p.Ser8ProfsTer2	frameshift_variant	1/8	1	NM_003000.3	ENSP00000364649	P1
SDHB	ENST00000466613.2	n.33del		non_coding_transcript_exon_variant	1/3	2
SDHB	ENST00000485515.5	n.9del		non_coding_transcript_exon_variant	1/7	5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 03, 2017

The c.21delC pathogenic mutation, located in coding exon 1 of the SDHB gene, results from a deletion of one nucleotide at nucleotide position 21, causing a translational frameshift with a predicted alternate stop codon (p.S8Pfs*2). In a study of 598 unrelated probands diagnosed with head and neck paraganglioma, this alteration was detected in 1 individuals (Neumann HP et al. Cancer Res. 2009 Apr;69:3650-6). 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. -

Hereditary pheochromocytoma-paraganglioma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Sep 12, 2024

The c.21del variant in the SDHB gene is located on the exon 1 and is predicted to shift of reading frame that introduces a premature translation termination codon (p.Ser8Profs*2), resulting in an absent or disrupted protein product. This variant has been reported in an individual with head and neck paraganglioma (PMID: 15328326, 19351833). Loss-of-function variants of SDHB are known to be pathogenic (PMID: 16258955, 19389109, 28490599). Other loss-of-function variants located in exon 1 (p.Ala25Glyfs*38, p.Leu9*, p.Met1Ile) have been reported in individuals with paraganglioma/pheochromocytoma and interpreted as pathogenic (ClinVar ID: 428928, 187527, 428932). This variant is absent in the general population database (gnomAD) and reported as pathogenic by one submitter in ClinVar (ID: 480807). Therefore, this variant is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs1553179359; hg19: chr1-17380493;