SPECC1L-ADORA2A

SPECC1L-ADORA2A readthrough (NMD candidate)

Basic information

Region (hg38): 22:24270898-24442356

Links

ENSG00000258555 ∙ NCBI:101730217 ∙ ∙ HGNC:49185 ∙ ∙ ∙ 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 SPECC1L-ADORA2A gene.

• not provided (156 variants)
• Inborn genetic diseases (47 variants)
• Teebi hypertelorism syndrome (17 variants)
• not specified (13 variants)
• Teebi hypertelorism syndrome 1 (11 variants)
• SPECC1L-related condition (11 variants)
• Autosomal dominant Opitz G/BBB syndrome (8 variants)
• Oculomaxillofacial dysostosis (5 variants)
• SPECC1L-related syndrome (2 variants)
• Oculomaxillofacial dysostosis;Teebi hypertelorism syndrome 1 (2 variants)
• Teebi hypertelorism syndrome 1;Oculomaxillofacial dysostosis (2 variants)
• Craniosynostosis syndrome (2 variants)
• Teebi hypertelorism syndrome;Autosomal dominant Opitz G/BBB syndrome (1 variants)
• Congenital omphalocele (1 variants)
• Malignant tumor of prostate (1 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPECC1L-ADORA2A 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)			7	6	1	14
splice region						0
non coding	7	7	109	56	40	219
Total	7	7	116	62	41

Variants in SPECC1L-ADORA2A

This is a list of pathogenic ClinVar variants found in the SPECC1L-ADORA2A region.

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

Position	Type	Phenotype	Significance	ClinVar
22-24302045-CA-C			Benign (May 19, 2021)
22-24302061-T-A			Benign (May 15, 2021)
22-24302187-T-C			Likely benign (Jul 01, 2022)
22-24302257-G-C			Uncertain significance (Apr 19, 2021)
22-24302272-T-C		Inborn genetic diseases	Uncertain significance (Aug 12, 2022)
22-24302276-T-C		SPECC1L-related disorder	Benign (Aug 01, 2024)
22-24302290-C-T		SPECC1L-related disorder	Likely benign (Oct 07, 2021)
22-24302291-G-T			Likely benign (Jan 21, 2022)
22-24302301-G-GA			Uncertain significance (Jan 21, 2024)
22-24302318-A-T		SPECC1L-related disorder	Uncertain significance (Apr 18, 2017)
22-24302337-A-G		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
22-24302362-G-A			Uncertain significance (Jul 06, 2022)
22-24302383-A-G		SPECC1L-related disorder	Uncertain significance (Feb 16, 2023)
22-24302389-T-G		Teebi hypertelorism syndrome 1;Oculomaxillofacial dysostosis • SPECC1L-related disorder	Likely benign (Aug 01, 2024)
22-24311999-C-T			Likely benign (Jul 01, 2024)
22-24312061-C-T			Uncertain significance (Dec 01, 2023)
22-24312075-C-T			Uncertain significance (Apr 01, 2023)
22-24313295-A-G			Likely benign (Mar 04, 2023)
22-24313314-C-G			Uncertain significance (Nov 27, 2023)
22-24313323-G-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
22-24313359-C-T		Teebi hypertelorism syndrome 1	Likely pathogenic (Jun 01, 2022)
22-24313360-G-A			Likely benign (Nov 01, 2022)
22-24313373-G-A			Uncertain significance (-)
22-24313389-G-A		Inborn genetic diseases	Uncertain significance (Jun 14, 2023)
22-24313392-C-T		Inborn genetic diseases	Uncertain significance (Jun 03, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.402

Gene ontology

• Biological process: actin cytoskeleton organization
• Cellular component: microtubule organizing center;filamentous actin