ZFPM1

zinc finger protein, FOG family member 1, the group of Zinc fingers C2HC-type|Zinc fingers C2H2-type|MicroRNA protein coding host genes|SET domain containing|PR/SET domain family

Basic information

Region (hg38): 16:88453280-88537031

Links

ENSG00000179588 ∙ NCBI:161882 ∙ OMIM:601950 ∙ HGNC:19762 ∙ Uniprot:Q8IX07 ∙ 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 ZFPM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFPM1 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				7	1	8
missense			117	2	3	122
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	118	9	4

Variants in ZFPM1

This is a list of pathogenic ClinVar variants found in the ZFPM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88485962-A-G			Benign (Mar 19, 2019)
16-88485971-G-A		not specified	Likely benign (May 08, 2024)
16-88485984-G-T		not specified	Uncertain significance (Oct 12, 2021)
16-88486010-A-C		not specified	Uncertain significance (Dec 13, 2023)
16-88486034-C-A		not specified	Uncertain significance (Sep 17, 2021)
16-88486040-G-A		not specified	Likely benign (Jun 14, 2024)
16-88489055-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-88489056-G-A			Likely benign (Dec 01, 2022)
16-88489094-G-C			Benign (Dec 31, 2019)
16-88489132-G-A		not specified	Likely benign (Feb 09, 2023)
16-88514400-G-A			Likely benign (Aug 01, 2022)
16-88526863-C-T		not specified	Uncertain significance (Sep 01, 2021)
16-88526888-C-T			Benign (Dec 31, 2019)
16-88528037-G-A		not specified	Uncertain significance (Jan 22, 2024)
16-88528070-G-A		not specified	Uncertain significance (Aug 30, 2022)
16-88528088-G-A		not specified	Uncertain significance (Mar 24, 2023)
16-88528091-C-T		not specified	Uncertain significance (Mar 28, 2024)
16-88528098-C-T		not specified	Uncertain significance (Jun 13, 2024)
16-88528103-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-88528136-A-G		not specified	Uncertain significance (Feb 23, 2023)
16-88528146-C-A		not specified	Uncertain significance (Feb 15, 2023)
16-88528225-C-T		not specified	Likely benign (Jan 03, 2024)
16-88528232-A-G		not specified	Likely benign (Jun 17, 2024)
16-88532046-G-A		not specified	Uncertain significance (Apr 07, 2022)
16-88532089-G-A		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFPM1	protein_coding	protein_coding	ENST00000319555	10	83700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.243	0.757	125242	0	69	125311	0.000275

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0470	437	434	1.01	0.0000276	6159
Missense in Polyphen		121	137.07	0.88274		1710
Synonymous	-2.64	253	205	1.23	0.0000149	2160
Loss of Function	3.52	6	25.0	0.240	0.00000116	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000202	0.000199
East Asian	0.00	0.00
Finnish	0.00288	0.00287
European (Non-Finnish)	0.0000268	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. Essential cofactor that acts via the formation of a heterodimer with transcription factors of the GATA family GATA1, GATA2 and GATA3. Such heterodimer can both activate or repress transcriptional activity, depending on the cell and promoter context. The heterodimer formed with GATA proteins is essential to activate expression of genes such as NFE2, ITGA2B, alpha- and beta-globin, while it represses expression of KLF1. May be involved in regulation of some genes in gonads. May also be involved in cardiac development, in a non-redundant way with ZFPM2/FOG2 (By similarity). {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;Factors involved in megakaryocyte development and platelet production;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Hemostasis;C-MYB transcription factor network;Transcriptional regulation by RUNX1;Signaling events mediated by HDAC Class I (Consensus)

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.670
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfpm1
• Phenotype: immune system phenotype; liver/biliary system phenotype; embryo phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: zfpm1
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;T-helper cell lineage commitment;outflow tract morphogenesis;atrioventricular valve morphogenesis;mitral valve formation;tricuspid valve formation;heart development;blood coagulation;regulation of definitive erythrocyte differentiation;erythrocyte differentiation;megakaryocyte differentiation;platelet formation;granulocyte differentiation;negative regulation of protein binding;regulation of chemokine production;embryonic hemopoiesis;megakaryocyte development;positive regulation of interferon-gamma biosynthetic process;negative regulation of interleukin-4 biosynthetic process;negative regulation of fat cell differentiation;regulation of megakaryocyte differentiation;cardiac muscle tissue morphogenesis;definitive erythrocyte differentiation;primitive erythrocyte differentiation;negative regulation of mast cell differentiation;ventricular septum morphogenesis;atrial septum morphogenesis;transcriptional activation by promoter-enhancer looping
• Cellular component: nucleus;nucleoplasm;transcription factor complex;transcriptional repressor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;RNA polymerase II activating transcription factor binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;transcription factor binding;metal ion binding