NBPF6

NBPF member 6, the group of NBPF members

Basic information

Region (hg38): 1:108450281-108471920

Links

ENSG00000186086 ∙ NCBI:653149 ∙ OMIM:613996 ∙ HGNC:31988 ∙ Uniprot:Q5VWK0 ∙ 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 NBPF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBPF6 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			17	6		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	6	0

Variants in NBPF6

This is a list of pathogenic ClinVar variants found in the NBPF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-108450632-G-A		not specified	Uncertain significance (Jul 16, 2021)
1-108450665-C-G		not specified	Likely benign (Dec 14, 2021)
1-108450674-C-T		not specified	Likely benign (Feb 28, 2023)
1-108450675-G-A		not specified	Uncertain significance (Jun 13, 2024)
1-108450690-A-C		not specified	Uncertain significance (Jul 20, 2022)
1-108450734-A-T		not specified	Likely benign (Nov 07, 2022)
1-108452246-A-G		not specified	Uncertain significance (Aug 02, 2023)
1-108465200-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-108465245-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-108465259-A-G		not specified	Likely benign (Apr 18, 2023)
1-108465287-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-108465302-G-C		not specified	Uncertain significance (Oct 26, 2022)
1-108465355-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-108467486-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-108467530-C-A		not specified	Uncertain significance (Dec 01, 2022)
1-108467561-C-T		not specified	Uncertain significance (Jul 26, 2022)
1-108467562-G-A		not specified	Likely benign (Jul 06, 2021)
1-108467587-G-C		not specified	Uncertain significance (Aug 22, 2023)
1-108467639-G-T		not specified	Uncertain significance (Oct 10, 2023)
1-108467651-G-A		not specified	Uncertain significance (May 05, 2023)
1-108470613-A-G		not specified	Likely benign (Mar 23, 2022)
1-108470617-G-C		not specified	Uncertain significance (Dec 19, 2022)
1-108470617-G-T		not specified	Uncertain significance (Mar 07, 2023)
1-108470628-T-A		not specified	Uncertain significance (Jun 18, 2024)
1-108470631-T-C		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBPF6	protein_coding	protein_coding	ENST00000444143	14	95204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0149	0.704	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.378	73	64.5	1.13	0.00000361	4150
Missense in Polyphen		12	10.863	1.1046		904
Synonymous	0.0998	23	23.6	0.974	0.00000115	1172
Loss of Function	0.646	3	4.47	0.671	2.09e-7	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0489

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm