MCF2L2

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

Basic information

Region (hg38): 3:183178040-183428778

Links

ENSG00000053524 ∙ NCBI:23101 ∙ OMIM:619946 ∙ HGNC:30319 ∙ Uniprot:Q86YR7 ∙ 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 MCF2L2 gene.

• Inborn genetic diseases (73 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCF2L2 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				2		2
missense			53	5		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			14	1		15
Total	0	0	67	8	0

Variants in MCF2L2

This is a list of pathogenic ClinVar variants found in the MCF2L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183179450-G-A		not specified	Uncertain significance (Aug 15, 2023)
3-183179491-G-T		not specified	Uncertain significance (Jun 18, 2021)
3-183179578-T-C		not specified	Uncertain significance (May 27, 2022)
3-183179655-G-A		not specified	Uncertain significance (Nov 10, 2022)
3-183179656-T-A		not specified	Uncertain significance (Jun 02, 2023)
3-183180117-T-A		not specified	Uncertain significance (Jul 19, 2022)
3-183193026-G-A		not specified	Uncertain significance (Jun 10, 2022)
3-183193071-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-183195225-G-A		not specified	Uncertain significance (Jun 21, 2023)
3-183206172-T-C		not specified	Uncertain significance (Aug 28, 2023)
3-183206183-C-A		not specified	Uncertain significance (Sep 01, 2021)
3-183206183-C-G		not specified	Uncertain significance (Jan 24, 2023)
3-183206187-C-T		not specified	Uncertain significance (Sep 14, 2022)
3-183207612-A-C		not specified	Uncertain significance (Dec 06, 2021)
3-183207628-T-C		not specified	Uncertain significance (Sep 26, 2022)
3-183207639-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-183207716-G-T		not specified	Uncertain significance (Feb 28, 2023)
3-183207729-C-T		not specified	Uncertain significance (Jan 24, 2023)
3-183207739-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-183207754-G-A		not specified	Uncertain significance (Sep 27, 2022)
3-183207787-C-G		not specified	Uncertain significance (Jun 16, 2022)
3-183207809-T-A		not specified	Uncertain significance (Feb 10, 2023)
3-183216009-C-T		not specified	Uncertain significance (Sep 07, 2022)
3-183216028-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-183219893-A-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCF2L2	protein_coding	protein_coding	ENST00000328913	30	250736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.16e-24	0.530	125589	0	159	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.786	559	614	0.911	0.0000327	7357
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00196	0.00195
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.000709	0.000707
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000414	0.000413
Middle Eastern	0.000709	0.000707
South Asian	0.000850	0.000850
Other	0.000658	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.573
• hipred: N
• hipred_score: 0.306
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.669

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of Rho protein signal transduction
• Molecular function: Rho guanyl-nucleotide exchange factor activity