PABPC4L

poly(A) binding protein cytoplasmic 4 like, the group of RNA binding motif containing

Basic information

Region (hg38): 4:134196332-134201789

Links

ENSG00000254535 ∙ NCBI:132430 ∙ ∙ HGNC:31955 ∙ Uniprot:P0CB38 ∙ 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 PABPC4L gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABPC4L 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	14	2	0

Variants in PABPC4L

This is a list of pathogenic ClinVar variants found in the PABPC4L region.

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

Position	Type	Phenotype	Significance	ClinVar
4-134199912-G-A		not specified	Likely benign (Mar 22, 2023)
4-134199984-T-C		not specified	Uncertain significance (Nov 14, 2023)
4-134200045-C-A		not specified	Uncertain significance (Jan 03, 2024)
4-134200092-G-C		not specified	Uncertain significance (Mar 27, 2023)
4-134200254-T-C		not specified	Uncertain significance (Mar 17, 2023)
4-134200304-C-T		not specified	Uncertain significance (Sep 23, 2023)
4-134200313-C-G		not specified	Uncertain significance (Nov 14, 2023)
4-134200329-C-A		not specified	Uncertain significance (Nov 30, 2022)
4-134200371-G-C		not specified	Uncertain significance (Mar 06, 2023)
4-134200414-A-T		not specified	Uncertain significance (Oct 13, 2023)
4-134200415-T-A		not specified	Uncertain significance (Aug 29, 2022)
4-134200491-C-A		not specified	Uncertain significance (Jan 23, 2024)
4-134200548-T-C		not specified	Uncertain significance (Mar 23, 2022)
4-134200608-C-T		not specified	Uncertain significance (Sep 26, 2022)
4-134200611-T-C		not specified	Uncertain significance (Jan 17, 2024)
4-134200700-T-C		not specified	Uncertain significance (Feb 15, 2023)
4-134200731-T-G		not specified	Uncertain significance (Nov 18, 2022)
4-134200769-A-G		not specified	Uncertain significance (Dec 20, 2023)
4-134200806-T-C		not specified	Uncertain significance (Mar 01, 2024)
4-134200869-G-T		not specified	Uncertain significance (May 23, 2023)
4-134200890-C-T		not specified	Uncertain significance (Dec 06, 2022)
4-134200914-C-T		not specified	Uncertain significance (Jun 23, 2023)
4-134200964-G-A		not specified	Uncertain significance (Jul 19, 2023)
4-134201003-T-C		not specified	Uncertain significance (May 26, 2023)
4-134201019-T-C		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABPC4L	protein_coding	protein_coding	ENST00000529122	1	5416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000533	0.897	108852	0	2	108854	0.00000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	175	239	0.732	0.0000127	2834
Missense in Polyphen		72	98.407	0.73165		1189
Synonymous	1.70	70	90.6	0.773	0.00000475	808
Loss of Function	1.45	7	12.6	0.558	8.96e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000793	0.0000780
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000622	0.0000617
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000622	0.0000617
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind RNA. {ECO:0000305}.
• Pathway: RNA degradation - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.411

Essentials

• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pabpc4l

Gene ontology

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