PUM2

pumilio RNA binding family member 2, the group of Pumilio homology domain containing

Basic information

Region (hg38): 2:20248691-20352234

Links

ENSG00000055917 ∙ NCBI:23369 ∙ OMIM:607205 ∙ HGNC:14958 ∙ Uniprot:Q8TB72 ∙ 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 PUM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUM2 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			65	1	1	67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	66	2	1

Variants in PUM2

This is a list of pathogenic ClinVar variants found in the PUM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-20251628-G-A		not specified	Benign (Dec 12, 2023)
2-20251661-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-20251684-G-A			Likely benign (Aug 01, 2022)
2-20251688-T-C		not specified	Uncertain significance (Jan 02, 2024)
2-20253830-T-C		not specified	Uncertain significance (May 18, 2023)
2-20253859-A-G		not specified	Uncertain significance (Jul 06, 2021)
2-20253860-T-C		not specified	Uncertain significance (Feb 06, 2024)
2-20253980-G-C		not specified	Uncertain significance (Aug 12, 2021)
2-20254929-T-C		not specified	Uncertain significance (Mar 04, 2024)
2-20254938-C-T		not specified	Uncertain significance (Dec 23, 2024)
2-20255242-G-A		not specified	Uncertain significance (Dec 04, 2024)
2-20255326-T-G		not specified	Uncertain significance (Oct 29, 2024)
2-20256052-A-G		not specified	Uncertain significance (Jan 18, 2025)
2-20258260-T-C		not specified	Uncertain significance (Dec 23, 2022)
2-20260434-G-A		not specified	Uncertain significance (Dec 03, 2024)
2-20260437-G-A		not specified	Uncertain significance (Mar 29, 2023)
2-20263229-T-A		not specified	Uncertain significance (Oct 19, 2024)
2-20263293-T-C		not specified	Uncertain significance (Dec 20, 2022)
2-20278619-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-20278679-G-A		not specified	Uncertain significance (Jul 16, 2024)
2-20278775-A-T		not specified	Uncertain significance (Nov 28, 2023)
2-20278782-C-A		not specified	Uncertain significance (Aug 02, 2023)
2-20282965-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-20282983-C-G		not specified	Uncertain significance (Feb 04, 2025)
2-20283000-C-T		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PUM2	protein_coding	protein_coding	ENST00000338086	20	103544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00508	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	408	584	0.699	0.0000301	6896
Missense in Polyphen		156	245.8	0.63467		2907
Synonymous	-1.06	221	202	1.10	0.0000102	2142
Loss of Function	5.77	9	55.3	0.163	0.00000290	635

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000631	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific RNA-binding protein that acts as a post-transcriptional repressor by binding the 3'-UTR of mRNA targets. Binds to an RNA consensus sequence, the Pumilio Response Element (PRE), 5'-UGUANAUA-3', that is related to the Nanos Response Element (NRE) (, PubMed:21397187). Mediates post- transcriptional repression of transcripts via different mechanisms: acts via direct recruitment of the CCR4-POP2-NOT deadenylase leading to translational inhibition and mRNA degradation (PubMed:22955276). Also mediates deadenylation- independent repression by promoting accessibility of miRNAs (PubMed:18776931, PubMed:22345517). Acts as a post-transcriptional repressor of E2F3 mRNAs by binding to its 3'-UTR and facilitating miRNA regulation (PubMed:22345517). Plays a role in cytoplasmic sensing of viral infection (PubMed:25340845). Represses a program of genes necessary to maintain genomic stability such as key mitotic, DNA repair and DNA replication factors. Its ability to repress those target mRNAs is regulated by the lncRNA NORAD (non- coding RNA activated by DNA damage) which, due to its high abundance and multitude of PUMILIO binding sites, is able to sequester a significant fraction of PUM1 and PUM2 in the cytoplasm (PubMed:26724866). May regulate DCUN1D3 mRNA levels (PubMed:25349211). May support proliferation and self-renewal of stem cells. Binds specifically to miRNA MIR199A precursor, with PUM1, regulates miRNA MIR199A expression at a postranscriptional level (PubMed:28431233). {ECO:0000269|PubMed:18776931, ECO:0000269|PubMed:21397187, ECO:0000269|PubMed:22345517, ECO:0000269|PubMed:22955276, ECO:0000269|PubMed:25340845, ECO:0000269|PubMed:25349211, ECO:0000269|PubMed:26724866, ECO:0000269|PubMed:28431233}.

Recessive Scores

• pRec: 0.0946

Intolerance Scores

• loftool: 0.375
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.769
• hipred: Y
• hipred_score: 0.768
• ghis: 0.683

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.800

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pum2
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: regulation of translation;posttranscriptional regulation of gene expression;stress granule assembly;production of miRNAs involved in gene silencing by miRNA;regulation of mRNA stability;regulation of chromosome segregation;regulation of gene silencing by miRNA;positive regulation of RIG-I signaling pathway;positive regulation of gene silencing by miRNA
• Cellular component: cytosol;cytoplasmic stress granule;nuclear membrane;perinuclear region of cytoplasm
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;miRNA binding