AGAP2-AS1

AGAP2 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 12:57726271-57728356

Links

ENSG00000255737 ∙ NCBI:100130776 ∙ ∙ HGNC:48633 ∙ ∙ ∙ 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 AGAP2-AS1 gene.

• Inborn genetic diseases (12 variants)
• AGAP2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP2-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			13			13
Total	0	0	13	0	0

Variants in AGAP2-AS1

This is a list of pathogenic ClinVar variants found in the AGAP2-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
12-57726635-T-C		not specified	Uncertain significance (May 10, 2022)
12-57726649-G-A		not specified	Uncertain significance (Mar 27, 2023)
12-57726658-G-C		not specified	Uncertain significance (Dec 21, 2022)
12-57726761-C-T		not specified	Uncertain significance (Sep 01, 2021)
12-57727000-C-T		not specified	Uncertain significance (Dec 27, 2022)
12-57727002-T-C		not specified	Uncertain significance (Jun 21, 2022)
12-57727022-G-A		AGAP2-related disorder	Likely benign (Mar 29, 2019)
12-57727112-G-C		not specified	Uncertain significance (Aug 11, 2022)
12-57727149-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-57727170-A-C		not specified	Uncertain significance (Jan 24, 2023)
12-57727427-C-A		not specified	Uncertain significance (Sep 16, 2021)
12-57727471-T-A		not specified	Uncertain significance (Aug 31, 2022)
12-57727489-C-A		AGAP2-related disorder	Uncertain significance (Apr 29, 2024)
12-57727491-A-T		AGAP2-related disorder	Likely benign (Apr 29, 2024)
12-57727704-A-G		not specified	Likely benign (Jan 29, 2024)
12-57727716-T-A		not specified	Uncertain significance (Apr 25, 2023)
12-57727974-A-G		not specified	Uncertain significance (Feb 13, 2024)
12-57728061-A-G		AGAP2-related disorder	Uncertain significance (Oct 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP2-AS1	protein_coding	protein_coding	ENST00000542466	1	2086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0275	0.926	125394	0	15	125409	0.0000598

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	84	175	0.481	0.0000110	1659
Missense in Polyphen		7	16.953	0.4129		142
Synonymous	2.44	55	83.3	0.661	0.00000574	593
Loss of Function	1.71	4	9.79	0.409	5.94e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000687	0.0000617
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000218	0.00000883
Middle Eastern	0.000544	0.000544
South Asian	0.000102	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.247

Gene Damage Prediction

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