COL27A1

collagen type XXVII alpha 1 chain, the group of MicroRNA protein coding host genes|Collagens

Basic information

Region (hg38): 9:114155537-114312511

Links

ENSG00000196739

∙ NCBI:85301 ∙ OMIM:608461 ∙ HGNC:22986 ∙ Uniprot:Q8IZC6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Steel syndrome (Strong), mode of inheritance: AR
Steel syndrome (Supportive), mode of inheritance: AR
Steel syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Steel syndrome	AR	Musculoskeletal	Outcomes have been described as better without the use of surgical treatment for hip dislocations	Craniofacial; Musculoskeletal	8423186; 24986830

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL27A1 gene.

not_provided (2091 variants)
Inborn_genetic_diseases (309 variants)
Steel_syndrome (56 variants)
not_specified (51 variants)
COL27A1-related_disorder (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL27A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032888.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	5 clinvar	864 clinvar	31 clinvar	901
missense	3 clinvar	3 clinvar	467 clinvar	96 clinvar	17 clinvar	586
nonsense	23 clinvar	8 clinvar				31
start loss						0
frameshift	46 clinvar	12 clinvar				58
splice donor/acceptor (+/-2bp)	5 clinvar	54 clinvar	2 clinvar	1 clinvar		62
Total	77	78	474	961	48

Highest pathogenic variant AF is 0.000057618603

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL27A1	protein_coding	protein_coding	ENST00000356083	61	156952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.586	0.414	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.629	1060	1.12e+3	0.947	0.0000709	11618
Missense in Polyphen		67	95.849	0.69902		966
Synonymous	-1.11	482	452	1.07	0.0000301	4090
Loss of Function	7.51	24	108	0.222	0.00000540	1246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role during the calcification of cartilage and the transition of cartilage to bone. {ECO:0000269|PubMed:17693149}.;
Disease: DISEASE: Steel syndrome (STLS) [MIM:615155]: A syndrome characterized by dislocated hips and radial heads, fusion of carpal bones, short stature, scoliosis, and cervical spine anomalies. Facial features include prominent forehead, long oval- shaped face, hypertelorism and broad nasal bridge. {ECO:0000269|PubMed:24986830}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Protein digestion and absorption - Homo sapiens (human);Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Intolerance Scores

loftool: 0.0176
rvis_EVS: 0.17
rvis_percentile_EVS: 65.34

Haploinsufficiency Scores

pHI: 0.701
hipred: N
hipred_score: 0.417
ghis: 0.517

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.145

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

Gene name: Col27a1
Phenotype: growth/size/body region phenotype; craniofacial phenotype; respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype; skeleton phenotype;

Zebrafish Information Network

Gene name: col27a1a
Affected structure: vertebral column
Phenotype tag: abnormal
Phenotype quality: curved lateral

Gene ontology

Biological process: growth plate cartilage chondrocyte development;extracellular matrix organization
Cellular component: extracellular region;fibrillar collagen trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
Molecular function: extracellular matrix structural constituent;extracellular matrix structural constituent conferring tensile strength;metal ion binding