ANGEL2

angel homolog 2

Basic information

Region (hg38): 1:212992182-213015867

Links

ENSG00000174606 ∙ NCBI:90806 ∙ OMIM:619001 ∙ HGNC:30534 ∙ Uniprot:Q5VTE6 ∙ 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 ANGEL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANGEL2 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	27	0	0

Variants in ANGEL2

This is a list of pathogenic ClinVar variants found in the ANGEL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-212995111-T-C		not specified	Uncertain significance (Feb 28, 2024)
1-212995115-C-T		not specified	Uncertain significance (Mar 08, 2024)
1-212995121-A-G		not specified	Uncertain significance (May 01, 2024)
1-212995175-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-212995184-C-G		not specified	Uncertain significance (Jan 26, 2022)
1-212997220-C-T		not specified	Uncertain significance (Sep 28, 2021)
1-212997259-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-213000911-A-T		not specified	Uncertain significance (Feb 05, 2024)
1-213005041-T-C		not specified	Uncertain significance (Apr 06, 2023)
1-213005157-T-A		not specified	Uncertain significance (Apr 04, 2023)
1-213005188-T-C		not specified	Uncertain significance (Aug 30, 2021)
1-213005241-G-A		not specified	Uncertain significance (Mar 29, 2023)
1-213005263-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-213005343-C-A		not specified	Uncertain significance (Feb 07, 2023)
1-213005344-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-213005404-C-T		not specified	Uncertain significance (Oct 20, 2021)
1-213005422-T-C		not specified	Uncertain significance (Sep 17, 2021)
1-213008277-C-T		not specified	Uncertain significance (Oct 03, 2023)
1-213008280-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-213008299-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-213008386-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-213008430-T-C		not specified	Uncertain significance (Jun 09, 2022)
1-213008464-C-T		not specified	Uncertain significance (Nov 21, 2022)
1-213013120-G-A		not specified	Uncertain significance (Aug 14, 2023)
1-213013281-T-C		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANGEL2	protein_coding	protein_coding	ENST00000366962	9	23645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000557	0.999	125600	0	148	125748	0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.882	247	289	0.854	0.0000144	3554
Missense in Polyphen		81	113.19	0.71564		1414
Synonymous	0.459	99	105	0.943	0.00000533	1019
Loss of Function	2.82	14	30.9	0.453	0.00000175	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000421	0.000421
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000761	0.000761
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000951	0.000950
Middle Eastern	0.000761	0.000761
South Asian	0.000231	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.406
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.0914
• hipred: N
• hipred_score: 0.426
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Angel2

Gene ontology

• Biological process: negative regulation of mitotic cell cycle;3'-UTR-mediated mRNA stabilization
• Cellular component: cytoplasm;Cajal body
• Molecular function: mRNA 3'-UTR binding