GDF5-AS1

GDF5 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 20:35433029-35435450

Previous symbols: [ "GDF5OS" ]

Links

ENSG00000204183 ∙ NCBI:554250 ∙ ∙ HGNC:33435 ∙ Uniprot:Q5U4N7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GDF5-AS1 gene.

• not provided (90 variants)
• Grebe syndrome (24 variants)
• Acromesomelic dysplasia 2B (22 variants)
• Multiple synostoses syndrome 2 (22 variants)
• Acromesomelic dysplasia 2C, Hunter-Thompson type (20 variants)
• Brachydactyly (19 variants)
• not specified (7 variants)
• Inborn genetic diseases (7 variants)
• Symphalangism, proximal, 1B (4 variants)
• - (3 variants)
• Brachydactyly type C (3 variants)
• Brachydactyly type A2 (2 variants)
• Brachydactyly type A1C (2 variants)
• GDF5-related condition (1 variants)
• 9 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDF5-AS1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	11	10	51	37	9	118
Total	11	10	51	37	9

Highest pathogenic variant AF is 0.0000131

Variants in GDF5-AS1

This is a list of pathogenic ClinVar variants found in the GDF5-AS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-35433389-A-G		Grebe syndrome • Acromesomelic dysplasia 2B • Brachydactyly • Multiple synostoses syndrome 2 • Acromesomelic dysplasia 2C, Hunter-Thompson type	Benign/Likely benign (Jan 13, 2018)
20-35433441-C-T		Grebe syndrome • Acromesomelic dysplasia 2B • Multiple synostoses syndrome 2 • Acromesomelic dysplasia 2C, Hunter-Thompson type • Brachydactyly	Benign/Likely benign (May 12, 2021)
20-35433484-A-G		Grebe syndrome • Acromesomelic dysplasia 2B • Brachydactyly • Multiple synostoses syndrome 2 • Acromesomelic dysplasia 2C, Hunter-Thompson type	Benign (May 12, 2021)
20-35433520-G-A		Acromesomelic dysplasia 2B • Multiple synostoses syndrome 2 • Acromesomelic dysplasia 2C, Hunter-Thompson type • Grebe syndrome • Brachydactyly	Benign/Likely benign (Jan 12, 2018)
20-35433522-A-G		Brachydactyly • Multiple synostoses syndrome 2 • Acromesomelic dysplasia 2B • Acromesomelic dysplasia 2C, Hunter-Thompson type • Grebe syndrome	Benign/Likely benign (Jan 13, 2018)
20-35433574-T-G		Acromesomelic dysplasia 2C, Hunter-Thompson type • Multiple synostoses syndrome 2 • Brachydactyly • Acromesomelic dysplasia 2B • Grebe syndrome	Benign (May 12, 2021)
20-35433650-C-G		Multiple synostoses syndrome 2 • Grebe syndrome • Brachydactyly • Acromesomelic dysplasia 2B • Acromesomelic dysplasia 2C, Hunter-Thompson type	Conflicting classifications of pathogenicity (Jan 12, 2018)
20-35433716-C-A		Acromesomelic dysplasia 2C, Hunter-Thompson type • Brachydactyly • Multiple synostoses syndrome 2 • Grebe syndrome • Acromesomelic dysplasia 2B	Benign (Sep 01, 2020)
20-35433743-C-T		Multiple synostoses syndrome 2 • Acromesomelic dysplasia 2B • Brachydactyly • Grebe syndrome • Acromesomelic dysplasia 2C, Hunter-Thompson type	Uncertain significance (Jan 13, 2018)
20-35433912-C-T			Likely benign (Dec 26, 2023)
20-35433915-G-A			Likely benign (Feb 04, 2023)
20-35433923-A-G			Uncertain significance (Sep 07, 2022)
20-35433924-C-A			Likely benign (Mar 23, 2022)
20-35433924-C-T			Likely benign (Jan 29, 2024)
20-35433927-C-T			Likely benign (Dec 09, 2023)
20-35433930-C-T			Likely benign (Jul 31, 2023)
20-35433932-C-A			Uncertain significance (Oct 07, 2023)
20-35433933-G-A			Likely benign (Dec 10, 2022)
20-35433939-G-A			Likely benign (Dec 04, 2023)
20-35433942-C-T			Likely benign (Jan 31, 2024)
20-35433944-C-T		Symphalangism, proximal, 1B	Pathogenic (Sep 01, 2006)
20-35433947-A-G			Uncertain significance (Aug 18, 2016)
20-35433947-ACTG-A			Uncertain significance (Jul 20, 2022)
20-35433948-C-T			Likely benign (Dec 20, 2023)
20-35433951-C-T			Likely benign (Mar 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDF5-AS1	protein_coding	protein_coding	ENST00000374375	1	2422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00264	0.805	125715	0	10	125725	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.814	136	165	0.822	0.0000124	1555
Missense in Polyphen		4	6.1774	0.64753		57
Synonymous	-0.962	88	77.2	1.14	0.00000543	568
Loss of Function	1.06	5	8.30	0.602	6.26e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000634	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0754
• hipred: N
• hipred_score: 0.235

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: mitochondrion