MCF2L2

protein-coding

MCF.2 cell line derived transforming sequence-like 2, the group of Dbl family Rho GEFs

Gene summary

Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015078.4

Inheritance

—

ClinVar variants

U:152B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr3:183,178,041-183,428,778

External References & Databases

Ensembl (ENSG00000053524)

Transcript & Mutation Effects

hg38 • Region Span ~250.7 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 MCF2L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 200

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015078.4. 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			2 clinvar	2 clinvar		4
missense			147 clinvar	13 clinvar		160
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	152	15	0	167

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015078.4	RefSeq	NP_055893.4	30	MANE Select
ENST00000328913.8	Ensembl	ENSP00000328118.3	30	MANE Select
ENST00000414362.6	Ensembl	ENSP00000414131.2	16	Standard
ENST00000414362.7	Ensembl	ENSP00000414131.2	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of Rho protein signal transduction

Molecular Function

Rho guanyl-nucleotide exchange factor activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328913
Coding exons: 30
Length: 250736
Individuals with no LoFs: 125589
Homozygous LoFs: 0
Heterozygous LoFs: 159
Defined: 125748
p: 0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.786	559	614	0.911	0.0000327	7357
Missense (PolyPhen)		112	145.65	0.76894		1880
Synonymous	1.70	198	231	0.858	0.0000131	2037
Loss of Function	2.20	48	67.5	0.711	0.00000354	774

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.0013	0.0013	notable
East Asian	0.00071	0.00071	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00041	0.00041	rare
South Asian	0.00085	0.00085	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably functions as a guanine nucleotide exchange factor. {ECO:0000250}.;

Recessive Scores

pRec: 0.0921

Intolerance Scores

LoFtool: 0.975
RVIS EVS: 0.85
RVIS percentile EVS: 88.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.669

Gene Damage Prediction

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