PABPN1L

PABPN1 like, cytoplasmic, the group of RNA binding motif containing

Basic information

Region (hg38): 16:88863333-88866660

Links

ENSG00000205022 ∙ NCBI:390748 ∙ ∙ HGNC:37237 ∙ Uniprot:A6NDY0 ∙ 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 PABPN1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABPN1L 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			44	2		46
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	0

Variants in PABPN1L

This is a list of pathogenic ClinVar variants found in the PABPN1L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88863773-A-G		not specified	Uncertain significance (Oct 16, 2024)
16-88863776-G-T		not specified	Uncertain significance (Jun 29, 2023)
16-88863790-C-T		not specified	Uncertain significance (Oct 08, 2024)
16-88863793-G-T		not specified	Uncertain significance (Feb 26, 2024)
16-88864261-C-T		not specified	Uncertain significance (Oct 04, 2024)
16-88864297-G-C		not specified	Likely benign (Jun 02, 2023)
16-88864301-C-T		not specified	Uncertain significance (Mar 10, 2025)
16-88864313-G-A		not specified	Uncertain significance (Apr 25, 2022)
16-88864316-G-A		not specified	Uncertain significance (Aug 08, 2022)
16-88864331-C-T		not specified	Uncertain significance (Jul 14, 2021)
16-88864334-G-A		not specified	Uncertain significance (Nov 15, 2024)
16-88864361-T-C		not specified	Uncertain significance (Oct 02, 2023)
16-88864366-C-G		not specified	Uncertain significance (Sep 20, 2023)
16-88864372-G-A		not specified	Uncertain significance (Jan 24, 2023)
16-88864373-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-88864863-C-T		not specified	Uncertain significance (Dec 01, 2022)
16-88864864-G-A		not specified	Uncertain significance (Feb 11, 2022)
16-88864864-G-C		not specified	Uncertain significance (Dec 19, 2023)
16-88864894-C-T		not specified	Uncertain significance (Sep 06, 2024)
16-88864897-C-T		not specified	Uncertain significance (Jan 19, 2022)
16-88864906-C-T		not specified	Uncertain significance (Jan 24, 2025)
16-88864914-T-G		not specified	Uncertain significance (Sep 01, 2021)
16-88864920-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-88865037-G-C		not specified	Uncertain significance (Mar 17, 2023)
16-88865039-G-T		not specified	Uncertain significance (Feb 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABPN1L	protein_coding	protein_coding	ENST00000419291	7	5035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-16	0.000707	123902	0	80	123982	0.000323

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.838	191	161	1.19	0.00000971	1741
Missense in Polyphen		34	34.008	0.99977		382
Synonymous	-1.20	84	71.1	1.18	0.00000489	541
Loss of Function	-1.42	21	15.1	1.39	8.86e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000958	0.000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.00170	0.00167
Finnish	0.00	0.00
European (Non-Finnish)	0.000232	0.000223
Middle Eastern	0.00170	0.00167
South Asian	0.000169	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds the poly(A) tail of mRNA. {ECO:0000250}.
• Pathway: Influenza A - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.686
• rvis_EVS: 1.62
• rvis_percentile_EVS: 96

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pabpn1l
• Phenotype: reproductive system phenotype

Gene ontology

• Cellular component: cytoplasm
• Molecular function: RNA binding