PMF1

polyamine modulated factor 1, the group of MIS12 kinetochore complex

Basic information

Region (hg38): 1:156212993-156240042

Links

ENSG00000160783 ∙ NCBI:11243 ∙ OMIM:609176 ∙ HGNC:9112 ∙ Uniprot:Q6P1K2 ∙ 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 PMF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PMF1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	9	0	0

Variants in PMF1

This is a list of pathogenic ClinVar variants found in the PMF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156213032-G-T		not specified	Uncertain significance (Jul 09, 2024)
1-156213157-A-C		not specified	Uncertain significance (Oct 07, 2024)
1-156225579-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-156225594-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-156225613-A-G		not specified	Uncertain significance (Jun 03, 2022)
1-156225640-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-156225643-C-T		not specified	Uncertain significance (Mar 20, 2024)
1-156232418-C-A		not specified	Uncertain significance (May 05, 2023)
1-156232423-C-T		not specified	Uncertain significance (Aug 04, 2024)
1-156236297-C-T			Likely benign (Oct 01, 2024)
1-156236298-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-156236316-C-G		not specified	Uncertain significance (Nov 26, 2024)
1-156236426-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-156236427-C-T		Inborn genetic diseases	Uncertain significance (Mar 20, 2023)
1-156239554-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-156239593-C-T		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PMF1	protein_coding	protein_coding	ENST00000567140	7	30091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.07e-8	0.184	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.346	140	129	1.09	0.00000677	1427
Missense in Polyphen		34	42.394	0.80199		491
Synonymous	0.0217	50	50.2	0.996	0.00000288	404
Loss of Function	0.326	13	14.3	0.907	6.97e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000418	0.000412
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis. May act as a cotranscription partner of NFE2L2 involved in regulation of polyamine-induced transcription of SSAT. {ECO:0000269|PubMed:10419538, ECO:0000269|PubMed:11256947, ECO:0000269|PubMed:15502821, ECO:0000269|PubMed:16585270}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.262

Intolerance Scores

• loftool: 0.697
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.07

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.551
• ghis: 0.460

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pmf1

Gene ontology

• Biological process: transcription by RNA polymerase II;cell cycle;chromosome segregation;cell division;positive regulation of nucleic acid-templated transcription
• Cellular component: MIS12/MIND type complex;condensed chromosome kinetochore;nuclear MIS12/MIND complex;nucleoplasm;transcription factor complex;Golgi apparatus;cytosol;intracellular membrane-bounded organelle
• Molecular function: transcription coactivator activity;protein binding;leucine zipper domain binding