BCL2L2-PABPN1

BCL2L2-PABPN1 readthrough

Basic information

Region (hg38): 14:23306833-23326175

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 (5 variants)
• Oculopharyngeal muscular dystrophy (3 variants)
• Oculopharyngeal muscular dystrophy 1 (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. These statistics are base on transcript: . Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		1	2
missense			10			10
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	12	0	1

Highest pathogenic variant AF is 0.0000531053

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