ESM1

endothelial cell specific molecule 1

Basic information

Region (hg38): 5:54977867-55022671

Links

ENSG00000164283 ∙ NCBI:11082 ∙ OMIM:601521 ∙ HGNC:3466 ∙ Uniprot:Q9NQ30 ∙ 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 ESM1 gene.

• not_specified (16 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007036.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			12	4		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	12	4	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESM1	protein_coding	protein_coding	ENST00000381405	3	44808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.212	0.752	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.981	85	115	0.742	0.00000659	1208
Missense in Polyphen		25	46.137	0.54186		463
Synonymous	0.485	42	46.2	0.909	0.00000294	353
Loss of Function	1.75	2	6.99	0.286	3.46e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in angiogenesis; promotes angiogenic sprouting. May have potent implications in lung endothelial cell-leukocyte interactions. {ECO:0000269|PubMed:20616313}.
• Pathway: Gastric Cancer Network 1 (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.325
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.385
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esm1

Gene ontology

• Biological process: angiogenesis;regulation of cell growth;sprouting angiogenesis;positive regulation of cell population proliferation;positive regulation of hepatocyte growth factor receptor signaling pathway
• Cellular component: extracellular region
• Molecular function: hepatocyte growth factor receptor binding;integrin binding;insulin-like growth factor binding