NIPSNAP3A

nipsnap homolog 3A

Basic information

Region (hg38): 9:104747682-104760120

Links

ENSG00000136783 ∙ NCBI:25934 ∙ OMIM:608871 ∙ HGNC:23619 ∙ Uniprot:Q9UFN0 ∙ 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 NIPSNAP3A gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPSNAP3A 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in NIPSNAP3A

This is a list of pathogenic ClinVar variants found in the NIPSNAP3A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-104747814-C-A		not specified	Uncertain significance (Apr 13, 2022)
9-104750996-G-C		not specified	Uncertain significance (Jul 25, 2023)
9-104751005-A-G		not specified	Uncertain significance (Nov 18, 2023)
9-104751082-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-104753031-C-G		not specified	Uncertain significance (Jul 05, 2022)
9-104753037-T-G		not specified	Uncertain significance (Aug 09, 2021)
9-104753041-A-T		not specified	Uncertain significance (Nov 13, 2023)
9-104754572-T-C		not specified	Uncertain significance (Oct 03, 2023)
9-104754605-G-A		not specified	Uncertain significance (Dec 21, 2023)
9-104754647-G-A		not specified	Uncertain significance (Feb 06, 2024)
9-104754677-C-T		not specified	Uncertain significance (Dec 06, 2021)
9-104754685-G-A		not specified	Uncertain significance (May 09, 2023)
9-104759116-T-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPSNAP3A	protein_coding	protein_coding	ENST00000374767	6	12435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.27e-12	0.00973	124947	6	795	125748	0.00319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.295	144	134	1.07	0.00000689	1599
Missense in Polyphen		49	40.848	1.1996		493
Synonymous	-0.474	54	49.7	1.09	0.00000265	479
Loss of Function	-0.828	16	12.8	1.25	5.45e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0296	0.0297
Ashkenazi Jewish	0.00566	0.00567
East Asian	0.000491	0.000489
Finnish	0.000370	0.000370
European (Non-Finnish)	0.00162	0.00160
Middle Eastern	0.000491	0.000489
South Asian	0.000328	0.000294
Other	0.00179	0.00179

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0977

Intolerance Scores

• loftool: 0.686
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.0867
• hipred: N
• hipred_score: 0.112
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipsnap3b

Gene ontology

• Cellular component: nucleus;mitochondrion;cytosol
• Molecular function: protein binding