ESAM

endothelial cell adhesion molecule, the group of V-set domain containing|IgCAM CXADR-related subfamily

Basic information

Region (hg38): 11:124752583-124762290

Links

ENSG00000149564 ∙ NCBI:90952 ∙ OMIM:614281 ∙ HGNC:17474 ∙ Uniprot:Q96AP7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schizophrenia; Neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic; Ophthalmologic	21822266; 36996813,

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ESAM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESAM 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			28	1		29
nonsense		2				2
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding					1	1
Total	0	5	28	2	1

Variants in ESAM

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

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

Position	Type	Phenotype	Significance	ClinVar
11-124753704-C-T		not specified	Uncertain significance (Oct 04, 2022)
11-124753786-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-124753833-C-T		not specified	Uncertain significance (Aug 17, 2022)
11-124753834-C-G		not specified	Uncertain significance (Mar 23, 2022)
11-124753848-C-A		not specified	Uncertain significance (Dec 14, 2023)
11-124753870-G-A		Neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity	Likely pathogenic (Mar 29, 2024)
11-124753933-G-T		not specified	Uncertain significance (Nov 19, 2022)
11-124753951-T-C			Likely benign (Nov 01, 2024)
11-124754250-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-124754251-G-A		not specified	Uncertain significance (Jul 12, 2022)
11-124754251-G-C		not specified	Uncertain significance (Aug 09, 2021)
11-124754253-C-T		not specified	Uncertain significance (Jun 14, 2024)
11-124754319-G-A		not specified	Uncertain significance (May 13, 2024)
11-124754338-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-124754349-G-T			Benign (Apr 20, 2018)
11-124754659-T-C		not specified	Uncertain significance (Nov 19, 2022)
11-124754727-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-124754758-T-C		not specified	Uncertain significance (Nov 13, 2023)
11-124756270-C-T		not specified	Uncertain significance (Mar 16, 2022)
11-124756271-G-A			Likely benign (Mar 01, 2023)
11-124756285-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-124756299-A-G		not specified	Uncertain significance (Feb 06, 2024)
11-124756338-C-T		not specified	Likely benign (Jan 16, 2024)
11-124756339-G-A		not specified	Uncertain significance (Jun 22, 2023)
11-124756540-C-T		Neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity • See cases	Likely pathogenic (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESAM	protein_coding	protein_coding	ENST00000278927	7	10161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.202	0.796	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.461	238	219	1.09	0.0000113	2450
Missense in Polyphen		54	60.528	0.89214		723
Synonymous	0.224	91	93.8	0.971	0.00000463	884
Loss of Function	2.71	4	15.5	0.258	7.59e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000285	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000285	0.000272
South Asian	0.0000981	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can mediate aggregation most likely through a homophilic molecular interaction. {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.486
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.243
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.494

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esam
• Phenotype: neoplasm; 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); hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: esama
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: aggregated

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;leukocyte migration
• Cellular component: plasma membrane;adherens junction;bicellular tight junction;integral component of membrane