MCF2

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

Basic information

Region (hg38): X:139581769-139708216

Links

ENSG00000101977 ∙ NCBI:4168 ∙ OMIM:311030 ∙ HGNC:6940 ∙ Uniprot:P10911 ∙ 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 MCF2 gene.

• Inborn genetic diseases (24 variants)
• not provided (14 variants)
• not specified (1 variants)
• Failure to thrive;Hypotonia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCF2 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	2	3
missense			24	2	3	29
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	24	3	7

Variants in MCF2

This is a list of pathogenic ClinVar variants found in the MCF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-139582456-G-C			Benign (Dec 31, 2019)
X-139582477-T-C		not specified	Likely benign (Oct 05, 2023)
X-139582484-G-C		not specified	Uncertain significance (Jul 09, 2021)
X-139582502-C-T		not specified	Uncertain significance (Jan 20, 2023)
X-139585133-G-A		not specified	Uncertain significance (May 17, 2023)
X-139586473-G-A		not specified	Uncertain significance (May 22, 2023)
X-139587734-G-T		not specified	Uncertain significance (Oct 02, 2023)
X-139588447-TA-T			Benign (Aug 16, 2017)
X-139589842-A-G			Benign (Dec 31, 2019)
X-139589884-C-T		not specified	Uncertain significance (Dec 13, 2023)
X-139596585-G-A			Benign (Jun 13, 2019)
X-139596592-C-A		Failure to thrive;Hypotonia	Uncertain significance (-)
X-139596700-C-A			Benign (Feb 25, 2018)
X-139596716-T-C		not specified	Uncertain significance (Jan 02, 2024)
X-139596757-T-C		not specified	Uncertain significance (Jan 04, 2024)
X-139597520-C-T		not specified	Uncertain significance (Oct 25, 2022)
X-139598414-A-C		not specified	Uncertain significance (Nov 18, 2022)
X-139602417-C-T		not specified	Uncertain significance (Jul 06, 2021)
X-139602458-T-C		not specified	Uncertain significance (Feb 05, 2024)
X-139602462-T-C		not specified	Likely benign (Apr 03, 2018)
X-139604725-A-C		not specified	Uncertain significance (Aug 02, 2023)
X-139604893-G-T		not specified	Uncertain significance (Apr 13, 2022)
X-139604909-G-C		not specified	Uncertain significance (Jan 16, 2024)
X-139607700-A-G		not specified	Uncertain significance (Jan 27, 2022)
X-139607755-C-T		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCF2	protein_coding	protein_coding	ENST00000519895	28	126458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0282	125696	5	5	125706	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	278	335	0.831	0.0000242	6637
Missense in Polyphen		80	117.12	0.68304		2381
Synonymous	0.125	113	115	0.985	0.00000830	1732
Loss of Function	4.99	7	41.9	0.167	0.00000305	794

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000162
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000795	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000495	0.0000352
Middle Eastern	0.0000795	0.0000544
South Asian	0.0000545	0.0000327
Other	0.000224	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) that modulates the Rho family of GTPases. Promotes the conversion of some member of the Rho family GTPase from the GDP-bound to the GTP-bound form. Isoform 1 exhibits no activity toward RHOA, RAC1 or CDC42. Isoform 2 exhibits decreased GEF activity toward CDC42. Isoform 3 exhibits a weak but significant activity toward RAC1 and CDC42. Isoform 4 exhibits significant activity toward RHOA and CDC42. The truncated DBL oncogene is active toward RHOA, RAC1 and CDC42.
• Disease: DISEASE: Note=MCF2 and DBL represent two activated versions of the same proto-oncogene. {ECO:0000305}.
• Pathway: Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Integrin;EGFR1;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;Axonal growth inhibition (RHOA activation);p75NTR regulates axonogenesis;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Regulation of CDC42 activity;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.414

Intolerance Scores

• loftool: 0.700
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.8

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.571
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.562

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mcf2
• 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)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;dendrite development;regulation of Rho protein signal transduction;intracellular signal transduction;positive regulation of apoptotic process;negative regulation of axonogenesis;regulation of small GTPase mediated signal transduction;cellular response to leukemia inhibitory factor
• Cellular component: cytosol;cytoskeleton;membrane
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding