AtlasGene
SDHC
succinate dehydrogenase complex subunit C
- HGNC 10682↗(opens in a new tab)
- Ensembl gene ENSG00000143252↗(opens in a new tab)
- NCBI Gene 6391↗(opens in a new tab)
Summary
- Cytogenetic location
- 1q23.3
- Coordinates
- Chromosome 1: 161,314,381–161,363,206 (GRCh38)
- Exons
- 6 exons across 48.8 kb
- Protein
- 169 amino acids
- Also known as
- CYB560, cybL
- Previous symbols
- PGL3
- MANE Select transcript
- ENST00000367975.7NM_003001.5
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Hereditary Gastrointestinal Stromal Tumour
- Autosomal dominant
Most GISTs are caused by changes acquired in the tumour itself. In familial GIST, a person inherits a change in one copy of KIT or PDGFRA that switches the gene on, or a change that stops SDHB or SDHC from working (Carney-Stratakis syndrome).
- 2 GenCC submitters rate it definitive or strong
▶Actionability
Specialist surveillance with endoscopy and imaging is offered, and SDHB or SDHC carriers are also screened for paragangliomas and phaeochromocytomas. Response to treatment varies by gene and genotype, and SDH-deficient GISTs generally respond poorly to standard tyrosine kinase inhibitors. Genetic counselling and testing of relatives are recommended.
Hereditary Pheochromocytoma and Paraganglioma
- Carney-Stratakis syndromeAutosomal dominant
A combination of paraganglioma and gastrointestinal stromal tumour caused by variants in the SDH genes.
- 1 GenCC submitter rates it definitive or strong
▶Actionability
Surveillance covers both paragangliomas and gastrointestinal stromal tumours.
- Hereditary pheochromocytoma-paragangliomaAutosomal dominant
A group of syndromes (PPGL types 1-7, TMEM127- and MAX-related) in which variants in SDHB, SDHD, SDHC, SDHA, SDHAF2, MAX or TMEM127 raise the risk of pheochromocytoma and paraganglioma.
- ClinGen rates the link definitive
- 4 GenCC submitters rate it definitive or strong
- On the ACMG secondary findings list
▶Actionability
Regular blood or urine metanephrine testing and periodic whole-body MRI help find tumours early, before they cause blood-pressure crises; relatives can be offered testing.
How SDHC is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
- Variants with a page
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 1.3 kb of the gene's 48.8 kb; 510 of those bases code for the protein.
Sequencing SDHC
64Hard
How hard SDHC is to sequence with short reads, out of 100
0 · Easy100 · Hard
Much of SDHC sits where short reads can miss or misplace a change.
What adds to it: the share of SDHC's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 100%.64%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 60%.0%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so reads from either may land on the other. Weight 60%.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 50%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 30%.1.3%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 20%.0%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of SDHC's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
84
positions in SDHC where ClinVar classes a change as pathogenic or likely pathogenic
16 of them (19%) fall in regions short reads find hard.
- Low mappabilityRegions where 100 bp or 250 bp reads cannot be placed uniquely. (16 sites)
A whole genome covers all 48.8 kb of SDHC, introns included, not only the 1.3 kb of exons.
Variants with a page (29)
The SDHC variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|
| c.1A>G | Exon 1 | 161,314,406 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.1A>T | Exon 1 | 161,314,406 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.2T>G | Exon 1 | 161,314,407 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.3G>A958G-A | Exon 1 | 161,314,408 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.21-2A>G | Intron 1 | 161,323,612 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.179+1G>C | Intron 3 | 161,328,498 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.179+1G>T | Intron 3 | 161,328,498 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.180-2A>G | Intron 3 | 161,340,592 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.242-2_242-1insG | Intron 4 | 161,356,675 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.386G>A | Exon 5 | 161,356,821 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
ClinVar pathogenic variants (109)
The SDHC variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 69
- Pathogenic/likely pathogenic 7
- Likely pathogenic 33
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_003001.5(SDHC):c.1A>G (p.Met1Val) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.1A>T (p.Met1Leu) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.2T>G (p.Met1Arg) | gastrointestinal stromal tumor and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.3G>A (p.Met1Ile) | gastrointestinal stromal tumor and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.43C>T (p.Arg15Ter) | Carney-Stratakis syndrome and 4 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.49del (p.His17fs) | pheochromocytoma/paraganglioma syndrome 3 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.118del (p.Arg40fs) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.177C>A (p.Tyr59Ter) | gastrointestinal stromal tumor and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.214C>T (p.Arg72Cys) | Carney-Stratakis syndrome and 4 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.3(SDHC):c.244dupG | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.250_251del (p.Leu84fs) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.248_251del (p.Ser83fs) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.376_391del (p.Tyr126fs) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.386G>A (p.Trp129Ter) | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.387G>A (p.Trp129Ter) | gastrointestinal stromal tumor and 3 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.397C>T (p.Arg133Ter) | Carney-Stratakis syndrome and 4 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.405+1G>T | gastrointestinal stromal tumor and 3 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.405+1G>C | gastrointestinal stromal tumor and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.17_18dup (p.Arg7Ter) | gastrointestinal stromal tumor and 1 other | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.21-2A>G | gastrointestinal stromal tumor and 2 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.148C>T (p.Arg50Cys) | Carney-Stratakis syndrome and 4 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.215G>A (p.Arg72His) | gastrointestinal stromal tumor and 3 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.278dup (p.Gly94fs) | gastrointestinal stromal tumor and 2 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.377A>G (p.Tyr126Cys) | Carney-Stratakis syndrome and 4 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_003001.5(SDHC):c.380A>G (p.His127Arg) | gastrointestinal stromal tumor and 3 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
See all 109 with every other SDHC variant in ClinVar → (opens in a new tab)
Genes linked to the same conditions
- SDHBsuccinate dehydrogenase complex iron sulfur subunit BShares 3 conditions
- SDHDsuccinate dehydrogenase complex subunit DShares 2 conditions
- KITKIT proto-oncogene, receptor tyrosine kinaseShares 1 condition
- MAXMYC associated transcriptional regulator XShares 1 condition
- PDGFRAplatelet derived growth factor receptor alphaShares 1 condition
- SDHAsuccinate dehydrogenase complex flavoprotein subunit AShares 1 condition
- SDHAF2succinate dehydrogenase complex assembly factor 2Shares 1 condition
- TMEM127transmembrane protein 127Shares 1 condition
Traits linked to SDHC
The Human Phenotype Ontology lists these as features of the rare conditions SDHC can cause. Each trait's page lists the other genes linked to it.
Abnormality of the endocrine system
- Paraganglioma
- Adrenal pheochromocytoma
- Extraadrenal pheochromocytoma
- Pheochromocytoma
- Adrenal overactivity
- Adrenocortical adenoma
- Paraganglioma of head and neck
- Chemodectoma
Show 2 more traits
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-19: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.19-9814e911.
Cite this page
Dante Labs. (n.d.). SDHC gene: succinate dehydrogenase complex subunit C. Retrieved 19 October 2026, from https://dantelabs.com/genes/sdhc
Dante Labs. SDHC gene: succinate dehydrogenase complex subunit C [Internet]. [cited 19 October 2026]. Available from: https://dantelabs.com/genes/sdhc
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