AtlasGene
B9D2
B9 domain containing 2
- HGNC 28636↗(opens in a new tab)
- Ensembl gene ENSG00000123810↗(opens in a new tab)
- NCBI Gene 80776↗(opens in a new tab)
Summary
- Cytogenetic location
- 19q13.2
- Coordinates
- Chromosome 19: 41,354,417–41,364,149 (GRCh38)
- Exons
- 4 exons across 9.7 kb
- Protein
- 175 amino acids
- Also known as
- MGC4093, MKS10, MKSR-2
- MANE Select transcript
- ENST00000243578.8NM_030578.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Joubert Syndrome And Related Disorders
- Joubert Syndrome
A ciliopathy defined by a malformation of the cerebellum and brainstem (the molar tooth sign), with low muscle tone, developmental delay and abnormal eye movements, sometimes with kidney, liver or eye involvement.
- 1 GenCC submitter rates it definitive or strong
Meckel Syndrome
- Autosomal recessive
A rare, lethal, genetic, multiple congenital anomaly disorder characterized by the triad of brain malformation mainly occipital encephalocele, large polycystic kidneys, and polydactyly as well as associated abnormalities that may include cleft lip/palate, cardiac and genital anomalies, central nervous system (CNS) malformations, liver fibrosis, and bone dysplasia.
- 1 GenCC submitter rates it definitive or strong
How B9D2 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 1 kb of the gene's 9.7 kb; 528 of those bases code for the protein.
Sequencing B9D2
4Easy
How hard B9D2 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of B9D2's exons sit where short reads map cleanly.
What adds to it: the share of B9D2'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 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.0%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.38%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.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 B9D2's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
7
positions in B9D2 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 9.7 kb of B9D2, introns included, not only the 1 kb of exons.
ClinVar pathogenic variants (7)
The B9D2 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 4
- Likely pathogenic 3
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_030578.4(B9D2):c.463G>A (p.Gly155Ser) (opens in a new tab) | Joubert syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_030578.4(B9D2):c.220C>T (p.Pro74Ser) (opens in a new tab) | Joubert syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_030578.4(B9D2):c.156_163del (p.Asp53fs) (opens in a new tab) | Joubert syndrome and 1 other | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_030578.4(B9D2):c.107T>C (p.Leu36Pro) (opens in a new tab) | Joubert syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_030578.4(B9D2):c.168C>G (p.Tyr56Ter) (opens in a new tab) | Meckel syndrome, type 10 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_030578.4(B9D2):c.127C>T (p.Gln43Ter) (opens in a new tab) | Meckel syndrome, type 10 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_030578.4(B9D2):c.15C>A (p.His5Gln) (opens in a new tab) | Meckel syndrome, type 10 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
- B9D1B9 domain containing 1Shares 2 conditions
- MKS1MKS transition zone complex subunit 1Shares 2 conditions
- RPGRIP1LRPGRIP1 likeShares 2 conditions
- TCTN2tectonic family member 2Shares 2 conditions
- TMEM107transmembrane protein 107Shares 2 conditions
- TMEM231transmembrane protein 231Shares 2 conditions
- TMEM67transmembrane protein 67Shares 2 conditions
- AHI1Abelson helper integration site 1Shares 1 condition
- ARL13BARF like GTPase 13BShares 1 condition
- ARL3ARF like GTPase 3Shares 1 condition
- ARMC9armadillo repeat containing 9Shares 1 condition
- CC2D2Acoiled-coil and C2 domain containing 2AShares 1 condition
Traits linked to B9D2
The Human Phenotype Ontology lists these as features of the rare conditions B9D2 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the genitourinary system
- Cystic kidney disease
- Hypospadias
- Short penis
- Multicystic kidney dysplasia
- Ambiguous external genitalia
- Undescended testes
- Double ureter
- Male pseudohermaphroditism
Show 2 more traits
Abnormality of limbs
- Extra little finger
- Extra toe attached near the little toe
- Postaxial polydactyly
- Ulnar deviation of the hand
- Talipes
- Bowing of the long bones
- Duplication of bones of the toes
- Extra finger
Show 1 more trait
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 2026-10-18: 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 2026.10.18-8b139e39.
Cite this page
Dante Labs. (n.d.). B9D2 gene: B9 domain containing 2. Retrieved 18 October 2026, from https://dantelabs.com/genes/b9d2
Dante Labs. B9D2 gene: B9 domain containing 2 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/b9d2
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