PABPC4

poly(A) binding protein cytoplasmic 4, the group of RNA binding motif containing|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:39560709-39576790

Links

ENSG00000090621 ∙ NCBI:8761 ∙ OMIM:603407 ∙ HGNC:8557 ∙ Uniprot:Q13310 ∙ 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 PABPC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABPC4 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in PABPC4

This is a list of pathogenic ClinVar variants found in the PABPC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-39561720-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-39562093-G-C		not specified	Uncertain significance (Aug 14, 2023)
1-39562407-G-C		not specified	Uncertain significance (Dec 07, 2021)
1-39563619-G-C		not specified	Uncertain significance (Sep 27, 2021)
1-39563657-G-A		not specified	Uncertain significance (Jul 21, 2021)
1-39563706-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-39563709-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-39563714-G-A		not specified	Uncertain significance (Oct 01, 2024)
1-39564453-G-A		not specified	Uncertain significance (Apr 14, 2022)
1-39564469-A-T		not specified	Likely benign (Jan 19, 2024)
1-39564495-T-G		not specified	Uncertain significance (Nov 30, 2022)
1-39565339-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-39568829-C-G		not specified	Uncertain significance (Oct 22, 2024)
1-39568893-A-G		not specified	Uncertain significance (Oct 13, 2023)
1-39568900-T-C		not specified	Likely benign (Mar 29, 2022)
1-39568928-C-G		not specified	Uncertain significance (Oct 09, 2024)
1-39569657-G-C		not specified	Uncertain significance (Sep 22, 2023)
1-39571241-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-39571337-C-T		not specified	Uncertain significance (Jan 04, 2025)
1-39575852-C-A		not specified	Uncertain significance (Dec 10, 2024)
1-39575935-C-G		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABPC4	protein_coding	protein_coding	ENST00000372858	15	15975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000951	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.92	233	397	0.587	0.0000223	4324
Missense in Polyphen		47	127.65	0.36818		1562
Synonymous	-1.67	168	143	1.18	0.00000780	1298
Loss of Function	4.87	3	33.4	0.0899	0.00000159	389

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo (By similarity). {ECO:0000250}.
• Pathway: RNA degradation - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.91
• rvis_percentile_EVS: 9.9

Haploinsufficiency Scores

• pHI: 0.969
• hipred: Y
• hipred_score: 0.811
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pabpc4
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: RNA processing;RNA catabolic process;translation;blood coagulation;regulation of mRNA stability;myeloid cell development
• Cellular component: nucleus;cytoplasm;cytosol;cytoplasmic stress granule;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;poly(A) binding;poly(U) RNA binding;poly(C) RNA binding