EML4

EMAP like 4, the group of EMAP like|WD repeat domain containing

Basic information

Region (hg38): 2:42169353-42332548

Previous symbols: [ "C2orf2" ]

Links

ENSG00000143924 ∙ NCBI:27436 ∙ OMIM:607442 ∙ HGNC:1316 ∙ Uniprot:Q9HC35 ∙ 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 EML4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EML4 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	2
missense			62	5	1	68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	62	6	3

Variants in EML4

This is a list of pathogenic ClinVar variants found in the EML4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-42245532-C-T		EML4-related disorder	Likely benign (Jun 14, 2022)
2-42256525-T-C		not specified	Uncertain significance (Jul 19, 2023)
2-42256546-A-G		not specified	Uncertain significance (Feb 17, 2022)
2-42256573-G-C		not specified	Uncertain significance (Jan 10, 2022)
2-42256603-A-C		not specified	Uncertain significance (Aug 04, 2023)
2-42261125-A-G		not specified	Uncertain significance (Mar 29, 2024)
2-42261162-A-G		not specified	Uncertain significance (Oct 12, 2021)
2-42261210-C-T		not specified	Uncertain significance (Apr 07, 2023)
2-42261219-C-G		not specified	Uncertain significance (Dec 28, 2022)
2-42261219-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-42261221-C-T		not specified	Uncertain significance (Sep 07, 2022)
2-42261255-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-42263216-C-G		not specified	Uncertain significance (Mar 15, 2024)
2-42263240-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-42263244-T-A		not specified	Uncertain significance (May 17, 2023)
2-42263249-T-G		not specified	Uncertain significance (Nov 17, 2023)
2-42263252-C-T		not specified	Likely benign (May 15, 2024)
2-42263277-A-C		not specified	Uncertain significance (Jan 03, 2024)
2-42263316-G-A			Benign (Jul 31, 2018)
2-42264719-A-G		not specified	Uncertain significance (Apr 18, 2023)
2-42280888-A-G		not specified	Uncertain significance (Sep 29, 2023)
2-42280895-T-C		not specified	Uncertain significance (May 31, 2024)
2-42280908-C-T			Benign (Jul 13, 2018)
2-42280928-A-T		not specified	Uncertain significance (Feb 28, 2023)
2-42280936-A-C		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EML4	protein_coding	protein_coding	ENST00000318522	23	163199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000482	1.00	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.367	548	524	1.05	0.0000263	6424
Missense in Polyphen		135	175.62	0.7687		2108
Synonymous	-2.99	236	184	1.28	0.00000982	1863
Loss of Function	4.84	17	56.1	0.303	0.00000321	628

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000240
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000483	0.0000462
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. {ECO:0000250}.
• Pathway: Non-small cell lung cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.761
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.63

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.492
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eml4

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process
• Cellular component: cytoplasm;microtubule;microtubule cytoskeleton;membrane
• Molecular function: molecular_function;microtubule binding