ANGPTL1

angiopoietin like 1, the group of Fibrinogen C domain containing|Angiopoietin like family|Receptor ligands

Basic information

Region (hg38): 1:178849534-178871077

Previous symbols: [ "ANGPT3" ]

Links

ENSG00000116194 ∙ NCBI:9068 ∙ OMIM:603874 ∙ HGNC:489 ∙ Uniprot:O95841 ∙ 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 ANGPTL1 gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANGPTL1 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					1	1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	1

Variants in ANGPTL1

This is a list of pathogenic ClinVar variants found in the ANGPTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-178851136-A-T		not specified	Uncertain significance (Jan 07, 2022)
1-178851148-A-G		not specified	Uncertain significance (Oct 03, 2022)
1-178851179-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-178851199-A-C		not specified	Uncertain significance (Jul 19, 2022)
1-178851296-T-C		not specified	Uncertain significance (Oct 03, 2022)
1-178851311-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-178852705-G-A			Benign (Feb 16, 2018)
1-178852710-G-C		not specified	Uncertain significance (Aug 29, 2022)
1-178852747-A-T		not specified	Uncertain significance (Dec 20, 2023)
1-178852761-C-T		not specified	Uncertain significance (May 11, 2022)
1-178852778-C-T		not specified	Uncertain significance (Jan 11, 2023)
1-178852812-G-A		not specified	Uncertain significance (Sep 21, 2023)
1-178852817-C-G		not specified	Uncertain significance (Mar 29, 2022)
1-178853598-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-178853635-C-G		not specified	Uncertain significance (Sep 16, 2021)
1-178853645-C-G		not specified	Uncertain significance (Jul 27, 2021)
1-178853704-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-178853707-T-G		not specified	Uncertain significance (Dec 28, 2023)
1-178853745-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-178853745-G-C		not specified	Uncertain significance (Dec 16, 2021)
1-178853772-C-T		not specified	Uncertain significance (May 27, 2022)
1-178864964-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-178864983-T-C		not specified	Uncertain significance (Aug 13, 2021)
1-178865014-G-C		not specified	Uncertain significance (Nov 13, 2023)
1-178865047-C-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANGPTL1	protein_coding	protein_coding	ENST00000234816	4	21348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-10	0.181	125623	0	123	125746	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	242	264	0.917	0.0000131	3267
Missense in Polyphen		88	110.26	0.79813		1354
Synonymous	0.0205	92	92.3	0.997	0.00000450	891
Loss of Function	0.627	17	20.0	0.849	9.31e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000385	0.000385
Ashkenazi Jewish	0.000389	0.000198
East Asian	0.000273	0.000272
Finnish	0.00378	0.00342
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.000273	0.000272
South Asian	0.000361	0.000359
Other	0.000532	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Rac1-Pak1-p38-MMP-2 pathway (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.658
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.251
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Angptl1
• Phenotype: normal phenotype

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway
• Cellular component: extracellular space;extracellular exosome
• Molecular function: signaling receptor binding