MCF2L

MCF.2 cell line derived transforming sequence like, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing

Basic information

Region (hg38): 13:112894377-113099742

Links

ENSG00000126217 ∙ NCBI:23263 ∙ OMIM:609499 ∙ HGNC:14576 ∙ Uniprot:O15068 ∙ 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 MCF2L gene.

• Inborn genetic diseases (48 variants)
• not provided (36 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCF2L 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				12	3	15
missense			44	10	3	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding				1	3	4
Total	0	0	44	23	9

Variants in MCF2L

This is a list of pathogenic ClinVar variants found in the MCF2L region.

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

Position	Type	Phenotype	Significance	ClinVar
13-112969383-A-C			Likely benign (Apr 01, 2023)
13-112969425-G-C		not specified	Uncertain significance (Sep 17, 2021)
13-112979696-C-A			Likely benign (Aug 01, 2022)
13-113012163-G-A			Likely benign (Sep 01, 2022)
13-113014783-A-T		not specified	Uncertain significance (Feb 28, 2023)
13-113014828-C-T		not specified	Uncertain significance (Jan 08, 2024)
13-113014845-C-T			Likely benign (Dec 31, 2019)
13-113024650-G-A		not specified	Uncertain significance (Apr 13, 2022)
13-113045281-G-A		not specified	Uncertain significance (Jan 03, 2024)
13-113045351-T-A		not specified	Uncertain significance (Nov 13, 2023)
13-113045368-G-C			Benign (May 18, 2018)
13-113060620-G-A		not specified	Uncertain significance (Dec 15, 2023)
13-113060626-G-A		not specified	Uncertain significance (Jan 31, 2022)
13-113060639-C-T		not specified	Uncertain significance (Feb 17, 2022)
13-113060642-G-A		not specified	Uncertain significance (May 18, 2022)
13-113060671-G-A		not specified	Uncertain significance (Feb 02, 2023)
13-113060694-C-A		not specified	Uncertain significance (Jun 21, 2022)
13-113064400-C-T		not specified	Uncertain significance (Aug 08, 2023)
13-113064401-G-A			Likely benign (Dec 31, 2019)
13-113064419-C-T		not specified	Uncertain significance (May 24, 2023)
13-113064941-C-G		not specified	Uncertain significance (Dec 14, 2023)
13-113064998-C-T			Likely benign (May 01, 2022)
13-113065029-G-T		not specified	Uncertain significance (Feb 27, 2024)
13-113065036-C-G		not specified	Uncertain significance (Mar 29, 2023)
13-113065045-C-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCF2L	protein_coding	protein_coding	ENST00000535094	30	205362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.72e-7	1.00	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	564	702	0.804	0.0000461	7331
Missense in Polyphen		105	195.88	0.53606		2113
Synonymous	0.290	310	317	0.979	0.0000239	2129
Loss of Function	4.86	24	67.0	0.358	0.00000331	750

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000360
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000321	0.000299
Middle Eastern	0.000164	0.000163
South Asian	0.000136	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor that catalyzes guanine nucleotide exchange on RHOA and CDC42, and thereby contributes to the regulation of RHOA and CDC42 signaling pathways (By similarity). Seems to lack activity with RAC1. Becomes activated and highly tumorigenic by truncation of the N-terminus (By similarity). Isoform 5 activates CDC42 (PubMed:15157669). {ECO:0000250|UniProtKB:Q63406, ECO:0000269|PubMed:15157669}.
• Pathway: Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Regulation of CDC42 activity;Neurotrophic factor-mediated Trk receptor signaling;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity (Consensus)

Intolerance Scores

• loftool: 0.715
• rvis_EVS: -1.58
• rvis_percentile_EVS: 3.14

Haploinsufficiency Scores

• pHI: 0.108
• hipred: Y
• hipred_score: 0.683
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.588

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mcf2l
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;regulation of Rho protein signal transduction;intracellular signal transduction;positive regulation of apoptotic process;regulation of small GTPase mediated signal transduction
• Cellular component: extracellular space;cytosol;plasma membrane;endomembrane system
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;phosphatidylinositol binding