NIPSNAP3B

protein-coding

nipsnap homolog 3B

Gene summary

NIPSNAP3B belongs to a family of proteins with putative roles in vesicular trafficking (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_018376.4

Inheritance

—

ClinVar variants

U:36B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr9:104,764,129-104,777,764

External References & Databases

Ensembl (ENSG00000165028)

Transcript & Mutation Effects

hg38 • Region Span ~13.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NIPSNAP3B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018376.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			34 clinvar	3 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	36	3	1	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018376.4	RefSeq	NP_060846.2	6	MANE Select
ENST00000374762.4	Ensembl	ENSP00000363894.3	6	MANE Select
ENST00000460936.5	Ensembl	ENSP00000435209.1	5	Standard
ENST00000900308.1	Ensembl	ENSP00000570367.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374762
Coding exons: 6
Length: 13301
Individuals with no LoFs: 125319
Homozygous LoFs: 3
Heterozygous LoFs: 425
Defined: 125747
p: 0.00170

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.278	130	139	0.934	0.00000757	1598
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.0020	0.0019	notable
Ashkenazi Jewish	0.0063	0.0063	notable
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00068	0.00068	rare
South Asian	0.0068	0.0068	notable
Other	0.0016	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.669
RVIS EVS: 1.35
RVIS percentile EVS: 94.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.107

Gene Damage Prediction

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