NDFIP2

Nedd4 family interacting protein 2

Basic information

Region (hg38): 13:79481155-79556077

Links

ENSG00000102471

∙ NCBI:54602 ∙ OMIM:610041 ∙ HGNC:18537 ∙ Uniprot:Q9NV92 ∙ 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 NDFIP2 gene.

not_specified (46 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDFIP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019080.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			41 clinvar	5 clinvar		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDFIP2	protein_coding	protein_coding	ENST00000218652	7	74924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.527	0.472	125710	0	4	125714	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.619	150	173	0.868	0.00000820	2114
Missense in Polyphen		22	55.093	0.39932		741
Synonymous	0.0832	69	69.9	0.987	0.00000393	675
Loss of Function	2.88	3	15.1	0.199	6.37e-7	188

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	0.0000462	0.0000462
European (Non-Finnish)	0.00000955	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.000194	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Activates HECT domain-containing E3 ubiquitin-protein ligases, including ITCH, NEDD4, NEDD4L, SMURF2, WWP1 and WWP2, and consequently modulates the stability of their targets. As a result, may control many cellular processes. Recruits ITCH, NEDD4 and SMURF2 to endosomal membranes. Negatively regulates KCNH2 potassium channel activity by decreasing its cell-surface expression and interfering with channel maturation through recruitment of NEDD4L to the Golgi apparatus and multivesicular body where it mediates KCNH2 degradation (PubMed:26363003). May modulate EGFR signaling. Together with NDFIP1, limits the cytokine signaling and expansion of effector Th2 T-cells by promoting degradation of JAK1, probably by ITCH- and NEDD4L-mediated ubiquitination (By similarity). {ECO:0000250|UniProtKB:Q91ZP6, ECO:0000269|PubMed:12761501, ECO:0000269|PubMed:19343052, ECO:0000269|PubMed:20534535, ECO:0000269|PubMed:26363003}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

loftool: 0.420
rvis_EVS: 0.33
rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

pHI: 0.145
hipred: Y
hipred_score: 0.804
ghis: 0.403

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.771

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ndfip2
Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype;

Gene ontology

Biological process: vacuolar transport;negative regulation of gene expression;metal ion transport;positive regulation of protein ubiquitination;negative regulation of transporter activity;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of protein transport
Cellular component: Golgi membrane;cytoplasm;mitochondrion;endoplasmic reticulum;Golgi apparatus;integral component of membrane;multivesicular body membrane;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
Molecular function: protein binding;WW domain binding