EML3

protein-coding

EMAP like 3, the group of WD repeat domain containing|EMAP like

Gene summary

Predicted to enable microtubule binding activity. Involved in mitotic metaphase chromosome alignment and regulation of mitotic spindle assembly. Located in several cellular components, including midbody; mitotic spindle microtubule; and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_153265.3

Inheritance

—

ClinVar variants

U:129B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr11:62,602,218-62,612,775

External References & Databases

Ensembl (ENSG00000149499)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EML3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 112

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153265.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar			4
missense			119 clinvar	1 clinvar		120
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	129	1	0	130

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 96 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153265.3	RefSeq	NP_694997.2	22	MANE Select
ENST00000394773.7	Ensembl	ENSP00000378254.2	22	MANE Select
NM_001300793.2	RefSeq	NP_001287722.1	22	Standard
NM_001300794.2	RefSeq	NP_001287723.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization

Molecular Function

microtubule binding

Cellular Component

cytoplasm
microtubule
microtubule cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394773
Coding exons: 22
Length: 10548
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125748
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.30	398	550	0.724	0.0000337	5686
Missense (PolyPhen)		141	258.79	0.54484		2656
Synonymous	1.46	195	223	0.875	0.0000134	1927
Loss of Function	3.97	18	47.5	0.379	0.00000251	501

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000073	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00031	0.00030	rare
East Asian	0.00016	0.00011	rare
Finnish	0.00040	0.00037	rare
European (Non-Finnish)	0.00024	0.00023	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. {ECO:0000250}.;

Recessive Scores

pRec: 0.0994

Intolerance Scores

LoFtool: 0.549
RVIS EVS: -0.84
RVIS percentile EVS: 11.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.473

Gene Damage Prediction

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