MLF1

myeloid leukemia factor 1

Basic information

Region (hg38): 3:158571163-158607252

Links

ENSG00000178053 ∙ NCBI:4291 ∙ OMIM:601402 ∙ HGNC:7125 ∙ Uniprot:P58340 ∙ 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 MLF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLF1 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	1
missense			14	1	3	18
nonsense				1		1
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	4

Variants in MLF1

This is a list of pathogenic ClinVar variants found in the MLF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-158592459-A-G		not specified	Uncertain significance (Dec 07, 2021)
3-158592466-G-A		not specified	Uncertain significance (Apr 07, 2022)
3-158592471-A-G		not specified	Uncertain significance (May 14, 2024)
3-158592564-G-T		not specified	Uncertain significance (Nov 14, 2023)
3-158593386-C-T		not specified	Likely benign (Aug 09, 2021)
3-158593387-G-T		MLF1-related disorder	Likely benign (Mar 03, 2020)
3-158593419-G-C		not specified	Uncertain significance (Aug 13, 2021)
3-158596889-A-G		not specified	Likely benign (Aug 14, 2024)
3-158596900-G-A			Benign (Dec 31, 2019)
3-158598086-C-T		not specified	Uncertain significance (Jun 11, 2021)
3-158598159-C-T		not specified	Uncertain significance (Jun 21, 2022)
3-158598183-C-A		not specified	Uncertain significance (Mar 25, 2024)
3-158598192-G-T		not specified	Uncertain significance (Oct 25, 2023)
3-158600032-G-A			Benign (May 09, 2018)
3-158600053-G-A		not specified	Uncertain significance (Jan 26, 2025)
3-158600067-G-A		not specified	Uncertain significance (Nov 09, 2024)
3-158600129-C-T		not specified	Uncertain significance (Aug 05, 2024)
3-158600160-C-T		MLF1-related disorder	Benign (Dec 31, 2019)
3-158602804-T-C		MLF1-related disorder	Likely benign (Mar 25, 2019)
3-158602808-T-C		MLF1-related disorder	Benign (Oct 17, 2019)
3-158602833-T-C		not specified	Uncertain significance (Apr 07, 2022)
3-158602905-C-T		not specified	Uncertain significance (Apr 24, 2023)
3-158602914-C-A		MLF1-related disorder	Benign (Oct 17, 2019)
3-158602923-C-T			Likely benign (Dec 31, 2019)
3-158605143-A-C		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLF1	protein_coding	protein_coding	ENST00000392822	8	36090

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.40e-9	0.364	125621	2	118	125741	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.587	129	149	0.865	0.00000723	1969
Missense in Polyphen		40	45.783	0.87368		632
Synonymous	1.55	33	46.4	0.711	0.00000214	525
Loss of Function	0.839	15	18.9	0.792	0.00000139	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00378	0.00365
Finnish	0.00	0.00
European (Non-Finnish)	0.000252	0.000237
Middle Eastern	0.00378	0.00365
South Asian	0.000594	0.000588
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in lineage commitment of primary hemopoietic progenitors by restricting erythroid formation and enhancing myeloid formation. Interferes with erythropoietin-induced erythroid terminal differentiation by preventing cells from exiting the cell cycle through suppression of CDKN1B/p27Kip1 levels. Suppresses COP1 activity via CSN3 which activates p53 and induces cell cycle arrest. Binds DNA and affects the expression of a number of genes so may function as a transcription factor in the nucleus. {ECO:0000269|PubMed:15861129}.
• Disease: DISEASE: Note=A chromosomal aberration involving MLF1 is a cause of myelodysplastic syndrome (MDS). Translocation t(3;5)(q25.1;q34) with NPM1/NPM. {ECO:0000269|PubMed:8570204}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.986
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.147
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.452

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mlf1

Gene ontology

• Biological process: myeloid progenitor cell differentiation;transcription, DNA-templated;regulation of transcription, DNA-templated;cell cycle arrest
• Cellular component: nucleus;cytoplasm;cilium;ciliary basal body
• Molecular function: DNA binding;protein binding;protein domain specific binding