AtlasGene
SPTB
spectrin beta, erythrocytic
- HGNC 11274↗(opens in a new tab)
- Ensembl gene ENSG00000070182↗(opens in a new tab)
- NCBI Gene 6710↗(opens in a new tab)
Summary
- Cytogenetic location
- 14q23.3
- Coordinates
- Chromosome 14: 64,746,283–64,879,907 (GRCh38)
- Exons
- 36 exons across 133.6 kb
- Protein
- 2,328 amino acids
- MANE Select transcript
- ENST00000644917.1NM_001355436.2
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
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library(jsonlite)
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Hereditary Spherocytosis
Hereditary spherocytosis is a congenital hemolytic anemia with a wide clinical spectrum (from symptom-free carriers to severe hemolysis) characterized by anemia, variable jaundice, splenomegaly and cholelithiasis.
- 2 GenCC submitters rate it definitive or strong
▶Actionability
Folic acid supplementation; splenectomy for moderate-severe disease (partial or total); pre-splenectomy vaccination; cholecystectomy for gallstones; transfusion support during aplastic crises; monitoring for parvovirus B19
Red Blood Cell Membrane Disorders
- Hereditary ElliptocytosisAutosomal dominant
Inherited changes in red cell skeleton proteins, mainly encoded by SPTA1, SPTB or EPB41, that make red cells oval or elongated; most people have no symptoms, but some have haemolytic anaemia.
- 2 GenCC submitters rate it definitive or strong
▶Actionability
Knowing about it explains unusual blood film findings and guides management of anaemia where present.
How SPTB is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 10.2 kb of the gene's 133.6 kb; 6,987 of those bases code for the protein.
Sequencing SPTB
4Easy
How hard SPTB is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of SPTB's exons sit where short reads map cleanly.
What adds to it: the share of SPTB'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%.0%
- 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%.1.5%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 20%.17%
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 SPTB'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.
110
positions in SPTB where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 133.6 kb of SPTB, introns included, not only the 10.2 kb of exons.
ClinVar pathogenic variants (112)
The SPTB 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 52
- Pathogenic/likely pathogenic 4
- Likely pathogenic 56
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_001355436.2(SPTB):c.5266C>T (p.Arg1756Ter) (opens in a new tab) | elliptocytosis 3 and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.4735C>T (p.Arg1579Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.2863C>T (p.Arg955Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.2521C>T (p.Gln841Ter) (opens in a new tab) | elliptocytosis 3 and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.4291C>T (p.Arg1431Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.4267C>T (p.Arg1423Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.3916C>T (p.Arg1306Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.189G>A (p.Trp63Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.6224A>G (p.Glu2075Gly) (opens in a new tab) | elliptocytosis 3 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.647G>A (p.Arg216Gln) (opens in a new tab) | elliptocytosis 3 and 1 other | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001355436.2(SPTB):c.6536_6537del (p.Val2179fs) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.6059_6060del (p.Val2020fs) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5794_5798+6del (opens in a new tab) | hemolytic anemia | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5788G>T (p.Glu1930Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5737dup (p.Arg1913fs) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5623C>T (p.Gln1875Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5506_5507insCGTCCAGCCCTTCCACC (p.Arg1836fs) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5464G>T (p.Glu1822Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5165_5166del (p.Asp1721_Phe1722insTer) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5114G>A (p.Trp1705Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.5099del (p.Asp1700fs) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.4969G>T (p.Glu1657Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.4942C>T (p.Gln1648Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.4873C>T (p.Arg1625Ter) (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001355436.2(SPTB):c.4842+1G>C (opens in a new tab) | hereditary spherocytosis type 2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
See all 112 with every other SPTB variant in ClinVar → (opens in a new tab)
Genes linked to the same conditions
- SLC4A1solute carrier family 4 member 1 (Diego blood group)Shares 2 conditions
- SPTA1spectrin alpha, erythrocytic 1Shares 2 conditions
- ANK1ankyrin 1Shares 1 condition
- EPB41erythrocyte membrane protein band 4.1Shares 1 condition
- EPB42erythrocyte membrane protein band 4.2Shares 1 condition
- SLC4A2solute carrier family 4 member 2Shares 1 condition
Traits linked to SPTB
The Human Phenotype Ontology lists these as features of the rare conditions SPTB can cause. Each trait's page lists the other genes linked to it.
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.). SPTB gene: spectrin beta, erythrocytic. Retrieved 19 October 2026, from https://dantelabs.com/genes/sptb
Dante Labs. SPTB gene: spectrin beta, erythrocytic [Internet]. [cited 19 October 2026]. Available from: https://dantelabs.com/genes/sptb
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