PABPC5

poly(A) binding protein cytoplasmic 5, the group of RNA binding motif containing

Basic information

Region (hg38): X:91434594-91438584

Links

ENSG00000174740 ∙ NCBI:140886 ∙ OMIM:300407 ∙ HGNC:13629 ∙ Uniprot:Q96DU9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PABPC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABPC5 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in PABPC5

This is a list of pathogenic ClinVar variants found in the PABPC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-91435582-G-A		not specified	Uncertain significance (Apr 25, 2023)
X-91435590-G-A		not specified	Uncertain significance (May 03, 2023)
X-91435796-G-C		not specified	Uncertain significance (Mar 16, 2024)
X-91435948-A-G		not specified	Uncertain significance (Jan 10, 2023)
X-91436070-A-C		not specified	Uncertain significance (Apr 08, 2024)
X-91436092-A-G		not specified	Uncertain significance (Jun 10, 2022)
X-91436264-A-C		not specified	Uncertain significance (Dec 27, 2023)
X-91436592-C-A		not specified	Uncertain significance (Jul 16, 2021)
X-91436691-C-A		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABPC5	protein_coding	protein_coding	ENST00000312600	1	3990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.893	0.106	125675	0	2	125677	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	94	165	0.571	0.0000136	2516
Missense in Polyphen		34	71.883	0.47299		1168
Synonymous	-0.319	67	63.8	1.05	0.00000517	767
Loss of Function	2.49	0	7.25	0.00	6.43e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.000134	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: 0.137

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.407
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pabpc5

Gene ontology

• Cellular component: nucleus;cytoplasm;mitochondrial matrix;cytosol;cytoplasmic stress granule;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;poly(A) binding;poly(U) RNA binding