EGFLAM

EGF like, fibronectin type III and laminin G domains, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 5:38258408-38465480

Links

ENSG00000164318 ∙ NCBI:133584 ∙ OMIM:617683 ∙ HGNC:26810 ∙ Uniprot:Q63HQ2 ∙ 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 EGFLAM gene.

• Inborn genetic diseases (46 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EGFLAM 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				2	1	3
missense			43	2	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	44	4	2

Variants in EGFLAM

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

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

Position	Type	Phenotype	Significance	ClinVar
5-38258768-G-A		not specified	Uncertain significance (Apr 18, 2023)
5-38337622-G-A		not specified	Uncertain significance (Mar 11, 2024)
5-38338750-G-A		not specified	Uncertain significance (Jan 02, 2024)
5-38338764-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-38338780-C-T		not specified	Uncertain significance (Jun 18, 2021)
5-38350502-A-G		not specified	Uncertain significance (Jun 06, 2023)
5-38350540-C-T		not specified	Uncertain significance (Dec 14, 2022)
5-38350591-C-A		not specified	Uncertain significance (Nov 19, 2022)
5-38350595-G-A		not specified	Likely benign (Jan 23, 2023)
5-38350602-C-G			Likely benign (May 01, 2022)
5-38352201-T-G		not specified	Uncertain significance (Mar 17, 2023)
5-38352210-C-A		not specified	Uncertain significance (Feb 27, 2024)
5-38352213-G-C		not specified	Uncertain significance (Jan 23, 2023)
5-38352247-C-T		not specified	Uncertain significance (Mar 24, 2023)
5-38352259-T-C		not specified	Uncertain significance (Apr 26, 2023)
5-38352286-G-C		not specified	Uncertain significance (Sep 06, 2022)
5-38370435-T-C			Benign (Jan 09, 2019)
5-38406158-C-T		not specified	Uncertain significance (Aug 10, 2021)
5-38406195-A-G		not specified	Uncertain significance (Feb 17, 2024)
5-38406218-G-T		not specified	Uncertain significance (May 18, 2022)
5-38406903-C-A		not specified	Uncertain significance (Jun 28, 2022)
5-38407071-T-C		not specified	Uncertain significance (Nov 08, 2022)
5-38407099-C-T		not specified	Uncertain significance (Aug 04, 2023)
5-38407119-G-A		not specified	Uncertain significance (Jan 19, 2022)
5-38407128-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EGFLAM	protein_coding	protein_coding	ENST00000354891	23	206613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.76e-19	0.628	125581	0	167	125748	0.000664

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	571	594	0.961	0.0000330	6635
Missense in Polyphen		196	224.7	0.87228		2615
Synonymous	-1.01	255	235	1.08	0.0000141	2008
Loss of Function	1.98	37	52.5	0.705	0.00000273	598

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00115	0.00113
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00123	0.00120
Finnish	0.000951	0.000832
European (Non-Finnish)	0.000331	0.000325
Middle Eastern	0.00123	0.00120
South Asian	0.00181	0.00180
Other	0.000503	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in both the retinal photoreceptor ribbon synapse formation and physiological functions of visual perception. Necessary for proper bipolar dendritic tip apposition to the photoreceptor ribbon synapse. Promotes matrix assembly and cell adhesiveness (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.738

Intolerance Scores

• loftool: 0.520
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.39

Haploinsufficiency Scores

• pHI: 0.219
• hipred: Y
• hipred_score: 0.604
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Egflam
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: positive regulation of cell-substrate adhesion;peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan;extracellular matrix organization
• Cellular component: basement membrane;interstitial matrix;cell junction;synapse
• Molecular function: calcium ion binding;glycosaminoglycan binding