ECSCR

endothelial cell surface expressed chemotaxis and apoptosis regulator

Basic information

Region (hg38): 5:139448560-139462743

Links

ENSG00000249751 ∙ NCBI:641700 ∙ OMIM:615736 ∙ HGNC:35454 ∙ Uniprot:Q19T08 ∙ 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 ECSCR gene.

Variants pathogenicity by type

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

Variants in ECSCR

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

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

Position	Type	Phenotype	Significance	ClinVar
5-139458153-G-T		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECSCR	protein_coding	protein_coding	ENST00000515823	4	58084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000425	0.429	124613	0	24	124637	0.0000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.775	24	37.3	0.643	0.00000168	444
Missense in Polyphen		6	4.2137	1.4239		38
Synonymous	-0.0337	16	15.8	1.01	8.53e-7	151
Loss of Function	0.0428	5	5.10	0.980	3.04e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000630	0.0000556
Finnish	0.000216	0.000186
European (Non-Finnish)	0.0000909	0.0000796
Middle Eastern	0.0000630	0.0000556
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates endothelial chemotaxis and tube formation. Has a role in angiogenesis and apoptosis via modulation of the actin cytoskeleton and facilitation of proteasomal degradation of the apoptosis inhibitors BIRC3/IAP1 and BIRC2/IAP2. {ECO:0000269|PubMed:18556573, ECO:0000269|PubMed:19416853}.

Haploinsufficiency Scores

• ghis: 0.547

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ecscr
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ecscr
• Affected structure: vascular cord
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: angiogenesis;apoptotic process;chemotaxis;negative regulation of angiogenesis;cell differentiation;positive regulation of proteasomal protein catabolic process;positive regulation of endothelial cell apoptotic process
• Cellular component: nucleoplasm;cytosol;plasma membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding