AtlasGene
NOG
noggin
- HGNC 7866↗(opens in a new tab)
- Ensembl gene ENSG00000183691↗(opens in a new tab)
- NCBI Gene 9241↗(opens in a new tab)
Summary
- Cytogenetic location
- 17q22
- Coordinates
- Chromosome 17: 56,593,699–56,595,611 (GRCh38)
- Exons
- 1 exon across 1.9 kb
- Protein
- 232 amino acids
- Previous symbols
- SYNS1, SYM1
- MANE Select transcript
- ENST00000332822.6NM_005450.6
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/nog.json"
page <- fromJSON(url)
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Get my Genome TestCurated reports relevant to this gene
Multiple Synostoses Syndrome (FGF9)
- Autosomal dominant
This form is caused by a change in one copy of the FGF9 gene, which encodes a growth factor important for skeletal development. Studied variants impair the protein's ability to pair up and bind its receptor, and they can be inherited from an affected parent or arise de novo.
- 2 GenCC submitters rate it definitive or strong
▶Actionability
Orthopaedic and hand assessment, with physiotherapy and occupational therapy to support function. Each child of an affected person has a 1 in 2 chance of inheriting the change, so genetic counselling and family testing can be offered.
NOG-Related Symphalangism Spectrum Disorder
- Autosomal dominant
Caused by changes in one copy of NOG, which encodes noggin, a protein that limits BMP signalling to allow joints to form. Changes can be inherited, and features vary within families.
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
▶Actionability
Hearing assessment, with hearing aids or stapes surgery for conductive hearing loss, and hand therapy or orthopaedic advice. Each child of an affected person may inherit the change, so genetic counselling and testing of relatives are offered.
How NOG is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
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 1.9 kb of the gene's 1.9 kb; 699 of those bases code for the protein.
Sequencing NOG
7Easy
How hard NOG is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of NOG's exons sit where short reads map cleanly.
What adds to it: the share of NOG'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%.9.3%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.60%
- 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 NOG'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.
10
positions in NOG 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 1.9 kb of NOG, introns included, not only the 1.9 kb of exons.
ClinVar pathogenic variants (10)
The NOG 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 6
- Likely pathogenic 4
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_005450.6(NOG):c.64dup (p.Ala22fs) (opens in a new tab) | multiple synostoses syndrome 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.104C>G (p.Pro35Arg) (opens in a new tab) | proximal symphalangism 1A and 1 other | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.379G>T (p.Glu127Ter) (opens in a new tab) | brachydactyly type B2 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.461del (p.Phe154fs) (opens in a new tab) | multiple synostoses syndrome 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.613dup (p.Trp205fs) (opens in a new tab) | stapes ankylosis with broad thumbs and toes | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.666C>G (p.Tyr222Ter) (opens in a new tab) | multiple synostoses syndrome 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.509del (p.Pro170fs) (opens in a new tab) | brachydactyly type B2 and 4 others | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.553T>C (p.Ser185Pro) (opens in a new tab) | stapes ankylosis with broad thumbs and toes | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.554C>G (p.Ser185Cys) (opens in a new tab) | proximal symphalangism 1A | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_005450.6(NOG):c.611G>A (p.Arg204Gln) (opens in a new tab) | tarsal-carpal coalition syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
Traits linked to NOG
The Human Phenotype Ontology lists these as features of the rare conditions NOG can cause. Each trait's page lists the other genes linked to it.
Abnormality of limbs
- Fused innermost hinge joints
- Fused outermost bones of hand
- Fused wrist bones
- Abnormality of the ankle
- Broad big toe
- Broad thumb
- Fused ankle bones
- Fused finger bones
Show 53 more traits
- Fusion of wrist bones
- Permanent flexion of the finger
- Short fingers or toes
- Short foot
- Short outermost bone of toe
- Short outermost finger bone
- Short palm
- Short toe
- Type B brachydactyly
- Abnormal shape of long bones of hand
- Absent phalangeal crease
- Absent proximal finger flexion creases
- Absent/small middle bones of toe
- Absent/small middle finger bone of the hand
- Absent/small outermost bones of toe
- Absent/small outermost finger bone of the hand
- Attachment of thumb close to wrist
- Bilateral single transverse palmar creases
- Curvature of finger
- Elbow ankylosis
- Elbow dislocation
- Finger syndactyly
- Fused innermost and middle bone of fourth finger
- Fused innermost and middle bones of little finger
- Fused long bone of hand with innermost finger bone
- Fused toes
- Radial deviation of finger
- Short middle bone of the little finger
- Shortened 1st long bone of hand
- Webbed fingers
- Webbed skin of toes
- Abnormality of the wrist
- Curvature of 4th toe
- Curvature of little finger
- Fused innermost and middle bones of 4th toe
- Fused innermost and middle pinkie toe bones
- Fusion of upper and lower arm bones
- Hypoplastic/small middle phalanx of the 5th toe
- Outward turned elbows
- Short middle bone of 4th finger
- Underdeveloped inner large forearm bone
- Absent outermost hand bone
- Curvature of digit
- Dislocated radial head
- Lower limb undergrowth
- Progressive fusion 2nd-5th proximal interphalangeal joints
- Short big toe
- Short finger
- Short humerus
- Short lower limbs
- Shortened 5th long bone of hand
- Single transverse palmar crease
- Webbed 2nd and 3rd toes
Abnormality of the musculoskeletal system
- Joint stiffness
- Proximal symphalangism
- Cone-shaped end part of bone
- Fused neck
- Enlargement of the costochondral junction
- Funnel chest
- Narrow spinal canal
- Short sternum
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.). NOG gene: noggin. Retrieved 19 October 2026, from https://dantelabs.com/genes/nog
Dante Labs. NOG gene: noggin [Internet]. [cited 19 October 2026]. Available from: https://dantelabs.com/genes/nog
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