ANGEL1

angel homolog 1

Basic information

Region (hg38): 14:76781733-76826246

Previous symbols: [ "KIAA0759" ]

Links

ENSG00000013523 ∙ NCBI:23357 ∙ OMIM:619537 ∙ HGNC:19961 ∙ Uniprot:Q9UNK9 ∙ 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 ANGEL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANGEL1 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			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in ANGEL1

This is a list of pathogenic ClinVar variants found in the ANGEL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-76789251-C-T		not specified	Uncertain significance (Oct 03, 2023)
14-76789269-A-C		not specified	Uncertain significance (Jun 10, 2024)
14-76789275-G-T		not specified	Uncertain significance (Mar 29, 2022)
14-76789292-G-C		not specified	Uncertain significance (Oct 03, 2022)
14-76790647-A-G		not specified	Uncertain significance (Apr 18, 2023)
14-76790704-G-A		not specified	Uncertain significance (Oct 26, 2021)
14-76790709-C-T		not specified	Likely benign (Sep 23, 2023)
14-76790711-C-G		not specified	Uncertain significance (Aug 08, 2023)
14-76791318-T-A		not specified	Uncertain significance (Oct 16, 2023)
14-76791321-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-76791357-G-A		not specified	Uncertain significance (Dec 20, 2022)
14-76803413-C-T		not specified	Uncertain significance (Sep 13, 2023)
14-76803428-C-A		not specified	Uncertain significance (Jun 10, 2024)
14-76803806-G-A		not specified	Uncertain significance (Oct 16, 2023)
14-76806502-C-T		not specified	Uncertain significance (Jan 24, 2023)
14-76806538-G-C		not specified	Uncertain significance (Mar 07, 2024)
14-76806561-G-A		not specified	Uncertain significance (Aug 31, 2022)
14-76806595-C-T		not specified	Uncertain significance (Dec 03, 2021)
14-76806619-T-C		not specified	Likely benign (Dec 27, 2023)
14-76806642-G-A		not specified	Uncertain significance (Dec 07, 2023)
14-76806642-G-T		not specified	Uncertain significance (Apr 07, 2023)
14-76806660-C-T		not specified	Uncertain significance (Feb 01, 2023)
14-76806676-C-T		not specified	Uncertain significance (Jan 30, 2024)
14-76806682-G-C		not specified	Uncertain significance (Jul 21, 2021)
14-76806766-G-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANGEL1	protein_coding	protein_coding	ENST00000251089	10	39002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.25e-9	0.996	125358	0	390	125748	0.00155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.924	331	382	0.867	0.0000209	4330
Missense in Polyphen		101	135.48	0.74547		1587
Synonymous	-0.0196	152	152	1.00	0.00000801	1366
Loss of Function	2.61	19	35.9	0.530	0.00000212	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00138
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000648	0.000647
European (Non-Finnish)	0.00151	0.00147
Middle Eastern	0.000109	0.000109
South Asian	0.00528	0.00527
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.655
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.3

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.150
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Angel1
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: nucleus;endoplasmic reticulum;cis-Golgi network;cytosol;perinuclear region of cytoplasm
• Molecular function: eukaryotic initiation factor 4E binding;protein domain specific binding