NBPF3

NBPF member 3, the group of NBPF members

Basic information

Region (hg38): 1:21440127-21485005

Links

ENSG00000142794 ∙ NCBI:84224 ∙ OMIM:612992 ∙ HGNC:25076 ∙ Uniprot:Q9H094 ∙ 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 NBPF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBPF3 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			24	3	1	28
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	25	4	1

Variants in NBPF3

This is a list of pathogenic ClinVar variants found in the NBPF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-21445088-T-C		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
1-21445184-G-T		not specified	Uncertain significance (Mar 30, 2024)
1-21445193-G-T		not specified	Uncertain significance (Mar 23, 2023)
1-21445207-C-G		not specified	Uncertain significance (Jan 10, 2022)
1-21468782-C-G		not specified	Uncertain significance (Oct 20, 2021)
1-21468793-C-T		not specified	Likely benign (May 08, 2024)
1-21468833-C-A		not specified	Uncertain significance (Oct 13, 2023)
1-21468837-A-G		not specified	Uncertain significance (Jan 05, 2022)
1-21468861-G-A		not specified	Uncertain significance (Nov 09, 2021)
1-21470678-G-C		not specified	Uncertain significance (Nov 10, 2022)
1-21470698-A-G		not specified	Uncertain significance (Mar 06, 2023)
1-21471649-C-G		not specified	Uncertain significance (Nov 03, 2023)
1-21471652-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-21471688-C-T		not specified	Uncertain significance (May 17, 2023)
1-21471690-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-21471706-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-21471714-C-T		not specified	Uncertain significance (May 27, 2022)
1-21471751-T-C		not specified	Uncertain significance (Jan 22, 2024)
1-21471765-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-21471769-A-C		not specified	Uncertain significance (Jan 25, 2024)
1-21471780-C-G		not specified	Uncertain significance (Sep 20, 2023)
1-21472905-T-C		not specified	Uncertain significance (Sep 25, 2023)
1-21472920-C-T			Benign (Dec 31, 2019)
1-21473459-C-T		not specified	Uncertain significance (Sep 14, 2022)
1-21473486-G-A		not specified	Likely benign (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBPF3	protein_coding	protein_coding	ENST00000318249	14	44878

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.08e-19	0.0286	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0301	307	306	1.00	0.0000157	4074
Missense in Polyphen		55	64.272	0.85574		987
Synonymous	1.18	105	122	0.864	0.00000676	1119
Loss of Function	0.823	31	36.4	0.853	0.00000201	414

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000354
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000479	0.0000462
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000163	0.000163
South Asian	0.000346	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.995
• rvis_EVS: 3.6
• rvis_percentile_EVS: 99.53

Haploinsufficiency Scores

• pHI: 0.0670
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm