PUM3

pumilio RNA binding family member 3, the group of Minor histocompatibility antigens|Pumilio homology domain containing

Basic information

Region (hg38): 9:2720469-2844095

Previous symbols: [ "KIAA0020" ]

Links

ENSG00000080608 ∙ NCBI:9933 ∙ OMIM:609960 ∙ HGNC:29676 ∙ Uniprot:Q15397 ∙ 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 PUM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUM3 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						0
missense			56	1	3	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	1	3

Variants in PUM3

This is a list of pathogenic ClinVar variants found in the PUM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-2729427-T-C			Likely benign (Sep 05, 2022)
9-2729427-T-G			Likely benign (Apr 24, 2021)
9-2729437-C-T		Cone dystrophy with supernormal rod response	Uncertain significance (Jan 13, 2018)
9-2729440-C-G			Likely benign (Jan 20, 2021)
9-2729442-A-G			Likely benign (Jun 05, 2022)
9-2729443-C-T			Uncertain significance (Jul 12, 2022)
9-2729460-C-T			Likely benign (Sep 21, 2022)
9-2729461-G-A			Uncertain significance (Sep 25, 2021)
9-2729461-G-C			Uncertain significance (Jan 28, 2021)
9-2729464-G-T			Uncertain significance (Jan 27, 2022)
9-2729465-G-A		Cone dystrophy with supernormal rod response	Pathogenic (Sep 01, 2006)
9-2729469-C-T			Likely benign (Aug 16, 2022)
9-2729470-G-A		Cone dystrophy with supernormal rod response • Retinal dystrophy • Abnormality of the nervous system;Nystagmus • KCNV2-related disorder	Pathogenic/Likely pathogenic (Dec 18, 2023)
9-2729470-G-T		KCNV2-related disorder	Conflicting classifications of pathogenicity (May 29, 2023)
9-2729472-AGAC-A		Retinal dystrophy	Uncertain significance (Feb 18, 2022)
9-2729475-C-T		not specified • Cone dystrophy with supernormal rod response	Benign (Jan 31, 2024)
9-2729477-T-C			Uncertain significance (Dec 03, 2021)
9-2729477-T-G		Retinal dystrophy	Uncertain significance (Jul 10, 2019)
9-2729480-A-G			Uncertain significance (Jun 20, 2022)
9-2729493-C-T			Likely benign (Mar 17, 2020)
9-2729497-G-A		Inborn genetic diseases	Uncertain significance (Nov 22, 2022)
9-2729497-G-C		Cone dystrophy with supernormal rod response	Likely pathogenic (-)
9-2729498-G-A			Uncertain significance (Jun 13, 2022)
9-2729500-A-T		Cone dystrophy with supernormal rod response	Uncertain significance (Oct 02, 2022)
9-2729502-G-A			Likely benign (Dec 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PUM3	protein_coding	protein_coding	ENST00000397885	17	123773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.21e-26	0.000124	125504	0	244	125748	0.000971

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.80	472	329	1.43	0.0000167	4251
Missense in Polyphen		65	45.437	1.4306		639
Synonymous	-2.88	162	122	1.33	0.00000672	1154
Loss of Function	-0.277	38	36.2	1.05	0.00000183	476

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00144	0.00140
Ashkenazi Jewish	0.000208	0.000198
East Asian	0.000885	0.000870
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00157	0.00153
Middle Eastern	0.000885	0.000870
South Asian	0.000561	0.000555
Other	0.000514	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the poly(ADP-ribosyl)ation activity of PARP1 and the degradation of PARP1 by CASP3 following genotoxic stress (PubMed:21266351). Binds to double-stranded RNA or DNA without sequence specificity (PubMed:25512524). Involved in development of the eye and of primordial germ cells (By similarity). {ECO:0000250|UniProtKB:X1WGX5, ECO:0000269|PubMed:21266351, ECO:0000269|PubMed:25512524}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.85

Haploinsufficiency Scores

• pHI: 0.653
• hipred: N
• hipred_score: 0.454
• ghis: 0.550

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Pum3

Zebrafish Information Network

• Gene name: pum3
• Affected structure: cone retinal bipolar cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: regulation of protein ADP-ribosylation
• Cellular component: nucleoplasm;chromosome;nucleolus;endoplasmic reticulum
• Molecular function: DNA binding;RNA binding;protein binding