BCL2L2-PABPN1

BCL2L2-PABPN1 readthrough

Basic information

Region (hg38): 14:23306832-23326175

Links

ENSG00000258643 ∙ NCBI:100529063 ∙ ∙ HGNC:42959 ∙ Uniprot:Q92843 ∙ 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 BCL2L2-PABPN1 gene.

• not provided (36 variants)
• Oculopharyngeal muscular dystrophy (20 variants)
• Inborn genetic diseases (14 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL2L2-PABPN1 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	2
missense			5			5
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding	8	2	22	6	13	51
Total	8	2	29	6	14

Highest pathogenic variant AF is 0.000331

Variants in BCL2L2-PABPN1

This is a list of pathogenic ClinVar variants found in the BCL2L2-PABPN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-23307940-G-A		not specified	Uncertain significance (Jun 16, 2023)
14-23308149-G-T		not specified	Uncertain significance (Aug 31, 2022)
14-23308829-C-T		not specified	Uncertain significance (Apr 18, 2023)
14-23308859-C-T		not specified	Uncertain significance (Jul 20, 2021)
14-23308865-G-A		not specified	Uncertain significance (Aug 02, 2021)
14-23308865-G-C		not specified	Uncertain significance (Mar 05, 2024)
14-23308939-G-A		not specified	Uncertain significance (Nov 10, 2022)
14-23319887-C-CTT			Benign (Mar 24, 2021)
14-23320430-A-AG			Benign (Apr 12, 2021)
14-23321310-A-G			Benign (Apr 13, 2021)
14-23321378-A-C			Likely benign (May 18, 2021)
14-23321469-G-T		Oculopharyngeal muscular dystrophy • PABPN1-related disorder	Conflicting classifications of pathogenicity (Jan 30, 2023)
14-23321471-TGGC-T		Oculopharyngeal muscular dystrophy	Uncertain significance (Sep 20, 2021)
14-23321471-T-TGGC		Oculopharyngeal muscular dystrophy • not specified	Conflicting classifications of pathogenicity (Aug 08, 2023)
14-23321471-T-TGGCGGC			Pathogenic (Apr 01, 2023)
14-23321471-T-TGGCGGCGGC		Oculopharyngeal muscular dystrophy • Oculopharyngeal muscular dystrophy 1 • Inborn genetic diseases	Pathogenic/Likely pathogenic (Feb 23, 2024)
14-23321471-T-TGGCGGCGGCGGCGGC		Oculopharyngeal muscular dystrophy	Pathogenic (Nov 01, 2022)
14-23321471-T-TGGCGGCGGCGGC		Oculopharyngeal muscular dystrophy	Pathogenic (Aug 08, 2023)
14-23321481-G-A			Likely benign (Feb 01, 2024)
14-23321481-G-GGCGGCGGCGGCA		Oculopharyngeal muscular dystrophy	Pathogenic/Likely pathogenic (Feb 01, 2024)
14-23321484-G-GGCGGCGGCA		Oculopharyngeal muscular dystrophy	Pathogenic/Likely pathogenic (Aug 08, 2023)
14-23321484-G-GGCGGCGGCAGCAGCA			Pathogenic (Aug 01, 2019)
14-23321486-C-T		Inborn genetic diseases	Uncertain significance (Feb 02, 2022)
14-23321487-G-GGCGGCA		Oculopharyngeal muscular dystrophy	Pathogenic (Aug 08, 2023)
14-23321490-G-GGCA		Oculopharyngeal muscular dystrophy	Pathogenic (Jan 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL2L2-PABPN1	protein_coding	protein_coding	ENST00000557008	7	18535

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.279	0.720	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	116	206	0.563	0.0000132	2151
Missense in Polyphen		28	72.089	0.38841		733
Synonymous	-1.06	86	74.3	1.16	0.00000409	682
Loss of Function	2.87	4	16.7	0.240	9.94e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000628	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell survival. Blocks dexamethasone-induced apoptosis. Mediates survival of postmitotic Sertoli cells by suppressing death-promoting activity of BAX. {ECO:0000269|PubMed:8761287}.
• Pathway: Influenza A - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.576
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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