NIPSNAP3B

nipsnap homolog 3B

Basic information

Region (hg38): 9:104764129-104777764

Links

ENSG00000165028 ∙ NCBI:55335 ∙ OMIM:608872 ∙ HGNC:23641 ∙ Uniprot:Q9BS92 ∙ 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 NIPSNAP3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPSNAP3B 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			17	2		19
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	2	1

Variants in NIPSNAP3B

This is a list of pathogenic ClinVar variants found in the NIPSNAP3B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-104764274-C-T		not specified	Uncertain significance (Aug 08, 2023)
9-104766353-G-C		not specified	Uncertain significance (Aug 22, 2023)
9-104766361-G-A		not specified	Likely benign (May 03, 2023)
9-104766416-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-104766494-T-C		not specified	Uncertain significance (Jun 03, 2022)
9-104766522-T-A		not specified	Uncertain significance (Nov 03, 2022)
9-104768880-G-C		not specified	Uncertain significance (Mar 01, 2023)
9-104768881-C-A		not specified	Uncertain significance (Dec 14, 2023)
9-104768890-G-A		not specified	Uncertain significance (Aug 21, 2023)
9-104768934-A-G		not specified	Uncertain significance (Jan 03, 2024)
9-104768950-G-A		not specified	Likely benign (May 01, 2022)
9-104768968-C-T		not specified	Uncertain significance (Dec 26, 2023)
9-104768977-C-T		not specified	Uncertain significance (Mar 06, 2023)
9-104768983-T-C		not specified	Uncertain significance (Nov 07, 2022)
9-104770881-C-G		not specified	Uncertain significance (Jan 26, 2023)
9-104770962-G-A		not specified	Uncertain significance (Dec 08, 2023)
9-104770963-G-C		not specified	Uncertain significance (Sep 17, 2021)
9-104772828-T-C		not specified	Uncertain significance (Feb 12, 2024)
9-104773004-A-G			Benign (Apr 04, 2018)
9-104773005-A-G		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPSNAP3B	protein_coding	protein_coding	ENST00000374762	6	13301

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.92e-10	0.0610	125319	3	425	125747	0.00170

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.278	130	139	0.934	0.00000757	1598
Missense in Polyphen		34	38.469	0.88382		461
Synonymous	0.129	49	50.2	0.977	0.00000278	465
Loss of Function	-0.139	14	13.5	1.04	6.32e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00208	0.00208
Ashkenazi Jewish	0.00627	0.00627
East Asian	0.000163	0.000163
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000681	0.000677
Middle Eastern	0.000163	0.000163
South Asian	0.00683	0.00675
Other	0.00165	0.00163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.669
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.35

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.132
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipsnap3b

Gene ontology

• Cellular component: mitochondrion