Vertebral column disorder

Summary

Vertebral column disorder (MONDO:0000812) is a disease (an umbrella term covering 15 Mondo subtypes) with 74 GWAS associations across 69 studies. A subtype of skeletal system disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 15 Mondo subtypes
• GWAS associations: 74

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	vertebral column disorder
Mondo ID	MONDO:0000812
MeSH	D013122
DOID	DOID:0060564
ICD-11	1989556002
SNOMED CT	699699005
UMLS	C0037933
MedGen	52455
Anatomy (UBERON)	UBERON:0001130
Is cancer (heuristic)	no

Also known as: disease of spine · disease of vertebral column · disease or disorder of vertebral column · disorder of vertebral column · vertebral column disease · vertebral column disease or disorder

Data availability: 74 GWAS associations (69 studies).

Disease family

This is a subtype of skeletal system disorder. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by body system or component › musculoskeletal system disorder › skeletal system disorder › vertebral column disorder

Related subtypes (47): symphalangism, cartilage cancer, patellar tendinitis, necrosis of ear ossicle, laryngeal cartilage cancer, ochronosis disorder, chondroma, periodontal disorder, posterior cranial fossa meningioma, anterior cranial fossa meningioma, middle cranial fossa meningioma, bone marrow disorder, cranial nodular fasciitis, flatfoot, bone disorder, skeletal tuberculosis, arthropathy, tooth disorder, primary basilar invagination, Brachymorphism-onychodysplasia-dysphalangism syndrome, cherubism, fibrodysplasia ossificans progressiva, Marfan syndrome, Buschke-Ollendorff syndrome, scalp defects-postaxial polydactyly syndrome, cartilage-hair hypoplasia, Teebi-Shaltout syndrome, short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome, ossification of the posterior longitudinal ligament of the spine, temtamy preaxial brachydactyly syndrome, metaphyseal undermodeling, spondylar dysplasia, and overgrowth, Al-Gazali syndrome, brachydactyly-syndactyly syndrome, endocrine-cerebro-osteodysplasia syndrome, metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria, multiple congenital anomalies-hypotonia-seizures syndrome 3, Rienhoff syndrome, Coffin-Siris syndrome, microcephaly-brachydactyly-kyphoscoliosis syndrome, cartilage development disorder, syndactyly, polydactyly, brachydactyly, sternal neoplasm, short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis, skeletal ligament disorder, brachydactyly-syndactyly-oligodactyly syndrome

Subtypes (15): spondylocostal dysostosis, sacrum chordoma, epidural spinal canal neoplasm, Baastrup syndrome, lumbosacral lipoma, spinal stenosis, intervertebral disk degenerative disorder, coccygodynia, vertebral joint disorder, sacrococcygeal teratoma, spinal cord injury, tuberculosis, spinal, vertebral disorder, lumbar disk disease, dropped head syndrome

Genetics & variants

GWAS landscape

74 GWAS associations across 69 studies. Top hits map to 14 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs183920372	1e-320	HLA-B	?
chr6:31359257	2e-49		A	0.24
chr10:72012403	3e-22		T	0.09
chr15:67073664	5e-18		C	0.08
chr10:72001257	8e-18		G	0.05
chr15:67370445	6e-17		G	0.05
chr12:23974404	2e-16		G	0.06
rs1498507	2e-16	SMAD3	A	0.04
rs6470764	4e-15	CCDC26	C	0.05
rs56290807	4e-15	SOX5	C	0.06
chr10:73764509	9e-15		C	0.04
chr12:23809619	4e-14		TAA	0.09
chr8:129707190	7e-14		G	0.08
rs1871452	9e-14	CHST3	T	0.04
rs13107325	4e-13	SLC39A8	C	0.07
rs565770962	4e-13	LINC01874	G	2.66
rs192568756	1e-12	PLXNA2	A	2.47
rs866932935	1e-12	LINC02028 - LINC02924	G	3.91
chr8:129727023	3e-12		CACACACACACAT	0.04
chr12:23822285	6e-12		T	0.05
rs112804589	8e-12	RNF217-AS1	A	3.1
rs534523711	8e-12	BMP8A	A	1.7
chr3:49437024	1e-11		T	0.04
rs187042787	1e-11	SAMD8	A	2.6
rs149495005	3e-11	DGKG	G	2.09
chr6:105383978	4e-11		C	0.04
rs532528082	4e-11	RNF13, ANKUB1	G	2.62
chr6:34696796	1e-10		AC	0.09
chr15:67075914	3e-10		CA	0.04
chr4:1184936	5e-10		CA	0.06

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90474078	UK Biobank Whole-Genome Sequencing Consortium	2025	93,732	364,708	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90476237	Verma A	2024	76,841	331,725	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90474063	UK Biobank Whole-Genome Sequencing Consortium	2025	48,510	409,930	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90038653	Donertas HM	2021	28,856	455,742	Common genetic associations between age-related diseases.
GCST90474083	UK Biobank Whole-Genome Sequencing Consortium	2025	26,978	431,462	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90478901	Verma A	2024	22,443	87,125	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90474056	UK Biobank Whole-Genome Sequencing Consortium	2025	11,553	446,887	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90478899	Verma A	2024	9,553	44,898	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90436665	Zhou W	2018	9,241	391,917	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90474060	UK Biobank Whole-Genome Sequencing Consortium	2025	6,651	451,789	Whole-genome sequencing of 490,640 UK Biobank participants.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	1
Tier 2: splice/UTR	1
Tier 3: regulatory	0
Tier 4: intronic/intergenic	48

MAF distribution

Bucket	Variants
common (>=0.05)	10
low_freq (0.01-0.05)	0
rare (<0.01)	8
unknown	32

Functional consequences

Consequence	Count
unknown	36
intron_variant	10
intergenic_variant	1
3_prime_UTR_variant	1
missense_variant	1
non_coding_transcript_exon_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs183920372	6	31359632	G>A		intron_variant	HLA-B	1e-320	Tier 4: intronic/intergenic
chr6:31359257							2e-49	Tier 4: intronic/intergenic
chr10:72012403							3e-22	Tier 4: intronic/intergenic
chr15:67073664							5e-18	Tier 4: intronic/intergenic
chr10:72001257							8e-18	Tier 4: intronic/intergenic
chr15:67370445				0.453			6e-17	Tier 4: intronic/intergenic
chr12:23974404				0.226			2e-16	Tier 4: intronic/intergenic
rs1498507	15	67075368	A>C	0.454	intron_variant	SMAD3	2e-16	Tier 4: intronic/intergenic
rs6470764	8	129713419	C>G,T	0.331	intergenic_variant	CCDC26	4e-15	Tier 4: intronic/intergenic
rs56290807	12	23819080	C>A	0.169	intron_variant	SOX5	4e-15	Tier 4: intronic/intergenic
chr10:73764509				0.406			9e-15	Tier 4: intronic/intergenic
chr12:23809619							4e-14	Tier 4: intronic/intergenic
chr8:129707190							7e-14	Tier 4: intronic/intergenic
rs1871452	10	72012903	T>A,G	0.369	3_prime_UTR_variant	CHST3	9e-14	Tier 2: splice/UTR
rs13107325	4	102267552	C>A,T	0.083	missense_variant	SLC39A8	4e-13	Tier 1: coding
rs565770962	2	503492	G>T	0	non_coding_transcript_exon_variant	LINC01874	4e-13	Tier 4: intronic/intergenic
rs192568756	1	208195776	A>G	0.001	intron_variant	PLXNA2	1e-12	Tier 4: intronic/intergenic
rs866932935	3	194096561	G>A	0	intron_variant	LINC02028 - LINC02924	1e-12	Tier 4: intronic/intergenic
chr8:129727023							3e-12	Tier 4: intronic/intergenic
chr12:23822285							6e-12	Tier 4: intronic/intergenic
rs112804589	6	124957064	A>G	0	intron_variant	RNF217-AS1	8e-12	Tier 4: intronic/intergenic
rs534523711	1	39506290	A>G	0.001	intron_variant	BMP8A	8e-12	Tier 4: intronic/intergenic
chr3:49437024				0.283			1e-11	Tier 4: intronic/intergenic
rs187042787	10	75157982	A>C	0	intron_variant	SAMD8	1e-11	Tier 4: intronic/intergenic
rs149495005	3	186151821	G>A	0.001	intron_variant	DGKG	3e-11	Tier 4: intronic/intergenic
chr6:105383978				0.314			4e-11	Tier 4: intronic/intergenic
rs532528082	3	149882283	G>A	0.001	intron_variant	RNF13, ANKUB1	4e-11	Tier 4: intronic/intergenic
chr6:34696796							1e-10	Tier 4: intronic/intergenic
chr15:67075914							3e-10	Tier 4: intronic/intergenic
chr4:1184936							5e-10	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 0.