NIPSNAP2

protein-coding

nipsnap homolog 2

Gene summary

This gene encodes a member of the NipSnap family of proteins that may be involved in vesicular transport. The encoded protein is localized to mitochondria and plays a role in oxidative phosphorylation. A pseudogene of this gene is located on the long arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

Previous symbols:

GBAS

MANE transcript

NM_001483.3

Inheritance

—

ClinVar variants

U:63B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr7:55,951,793-56,000,181

External References & Databases

Ensembl (ENSG00000146729)

Transcript & Mutation Effects

hg38 • Region Span ~48.4 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 NIPSNAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001483.3. 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			51 clinvar	1 clinvar		52
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	63	1	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001483.3	RefSeq	NP_001474.1	10	MANE Select
ENST00000322090.8	Ensembl	ENSP00000313050.3	10	MANE Select
NM_001202469.2	RefSeq	NP_001189398.1	8	Standard
ENST00000415967.2	Ensembl	ENSP00000409266.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

oxidative phosphorylation
mitochondrion organization
positive regulation of high voltage-gated calcium channel activity

Molecular Function

protein binding

Cellular Component

mitochondrion
mitochondrial outer membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000322090
Coding exons: 10
Length: 48389
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125747
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.34	99	144	0.687	0.00000784	1866
Missense (PolyPhen)		24	39.051	0.61458		421
Synonymous	-0.854	60	52.2	1.15	0.00000296	519
Loss of Function	1.15	15	20.6	0.727	0.00000103	234

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00029	0.00028	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a positive regulator of L-type calcium channels. {ECO:0000250|UniProtKB:O55126}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

RVIS EVS: 0.08
RVIS percentile EVS: 59.76

Essentials

Essential (gene trap): N