EFS

embryonal Fyn-associated substrate, the group of Cas scaffold proteins

Basic information

Region (hg38): 14:23356403-23365752

Links

ENSG00000100842 ∙ NCBI:10278 ∙ OMIM:609906 ∙ HGNC:16898 ∙ Uniprot:O43281 ∙ 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 EFS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFS 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			62			62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	0	1

Variants in EFS

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

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

Position	Type	Phenotype	Significance	ClinVar
14-23357230-G-A		not specified	Uncertain significance (Aug 10, 2024)
14-23357234-C-A		not specified	Uncertain significance (May 18, 2023)
14-23357238-G-C		not specified	Uncertain significance (Apr 17, 2023)
14-23357261-G-T		not specified	Uncertain significance (Sep 26, 2023)
14-23357330-C-T		not specified	Uncertain significance (Nov 30, 2022)
14-23357357-C-T		not specified	Uncertain significance (Aug 27, 2024)
14-23357429-C-G		not specified	Uncertain significance (Dec 02, 2021)
14-23357452-A-G		not specified	Uncertain significance (Jul 19, 2022)
14-23357453-C-A		not specified	Uncertain significance (Sep 27, 2022)
14-23357464-C-T		not specified	Uncertain significance (Feb 12, 2025)
14-23357501-C-T		not specified	Uncertain significance (Feb 16, 2023)
14-23357507-G-A		not specified	Uncertain significance (May 24, 2023)
14-23357512-G-T		not specified	Uncertain significance (Nov 10, 2023)
14-23357521-T-G		not specified	Uncertain significance (Dec 28, 2022)
14-23357578-C-T		not specified	Uncertain significance (Feb 22, 2023)
14-23357617-T-C		not specified	Uncertain significance (Oct 01, 2024)
14-23357621-C-T		not specified	Uncertain significance (Dec 02, 2021)
14-23357629-A-G		not specified	Uncertain significance (Mar 29, 2023)
14-23358938-G-C		not specified	Uncertain significance (May 08, 2023)
14-23358947-C-T		not specified	Uncertain significance (Sep 05, 2024)
14-23359369-T-C		not specified	Uncertain significance (Oct 03, 2022)
14-23359427-T-C		not specified	Uncertain significance (Jan 19, 2025)
14-23359432-C-A		not specified	Uncertain significance (Mar 06, 2023)
14-23359450-C-T		not specified	Uncertain significance (May 14, 2024)
14-23359451-G-A		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFS	protein_coding	protein_coding	ENST00000216733	6	9351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-8	0.421	125695	0	50	125745	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.385	297	316	0.939	0.0000179	3470
Missense in Polyphen		114	120.14	0.94891		1312
Synonymous	1.03	129	145	0.891	0.00000873	1315
Loss of Function	0.863	14	17.9	0.780	9.36e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000427
Ashkenazi Jewish	0.000219	0.000198
East Asian	0.000438	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000256	0.000246
Middle Eastern	0.000438	0.000435
South Asian	0.00	0.00
Other	0.000343	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Docking protein which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. May serve as an activator of SRC and a downstream effector. Interacts with the SH3 domain of FYN and with CRK, SRC, and YES (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.888
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.61

Haploinsufficiency Scores

• pHI: 0.411
• hipred: N
• hipred_score: 0.170
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.647

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Efs
• Phenotype: renal/urinary system phenotype; immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: cell adhesion;cell migration;intracellular signal transduction;actin filament reorganization
• Cellular component: cytoplasm;plasma membrane
• Molecular function: protein binding;SH3 domain binding;protein domain specific binding