NBPF20

NBPF member 20, the group of NBPF members

Basic information

Region (hg38): 1:145289899-145425603

Links

ENSG00000162825 ∙ NCBI:100288142 ∙ OMIM:614007 ∙ HGNC:32000 ∙ Uniprot:P0DPF2 ∙ 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 NBPF20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBPF20 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
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in NBPF20

This is a list of pathogenic ClinVar variants found in the NBPF20 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145291637-T-G			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBPF20	protein_coding	protein_coding	ENST00000369365	91	77674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-7	0.0340	120533	0	19	120552	0.0000788

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.88	75	30.4	2.47	0.00000140	24299
Missense in Polyphen		60	25.873	2.319		14469
Synonymous	-1.86	22	13.3	1.65	5.98e-7	6838
Loss of Function	-2.07	8	3.71	2.16	1.53e-7	3145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000245
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000164
Finnish	0.0000480	0.0000478
European (Non-Finnish)	0.000117	0.000102
Middle Eastern	0.000168	0.000164
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.394

Essentials

• 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

Gene ontology

• Cellular component: cytoplasm