NDFIP1

protein-coding

Nedd4 family interacting protein 1

Gene summary

The protein encoded by this gene belongs to a small group of evolutionarily conserved proteins with three transmembrane domains. It is a potential target for ubiquitination by the Nedd4 family of proteins. This protein is thought to be part of a family of integral Golgi membrane proteins. [provided by RefSeq, Jul 2008]

MANE transcript

NM_030571.4

Inheritance

—

ClinVar variants

U:14B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:142,108,779-142,154,440

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~45.7 kb
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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 NDFIP1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 11
not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030571.4. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
12
clinvar
12
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00140115
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_030571.4RefSeqNP_085048.17MANE Select
ENST00000253814.6EnsemblENSP00000253814.37MANE Select
ENST00000856977.1EnsemblENSP00000527036.17Standard
ENST00000856977.2EnsemblENSP00000527036.17Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • regulation of myeloid leukocyte differentiation
  • negative regulation of type 2 immune response
  • cellular iron ion homeostasis
  • vacuolar transport
  • negative regulation of gene expression

Molecular Function

  • protein binding
  • WW domain binding

Cellular Component

  • Golgi membrane
  • extracellular region
  • Golgi apparatus
  • cell cortex
  • endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000253814
Coding exons
7
Length
45936
Individuals with no LoFs
125689
Homozygous LoFs
0
Heterozygous LoFs
3
Defined
125692
p
0.0000119
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.50651090.5970.000005121439
Missense (PolyPhen)2256.1450.39184729
Synonymous-0.07754039.41.020.00000188426
Loss of Function3.16011.60.004.91e-7155

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.0000990.000099rare
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Activates HECT domain-containing E3 ubiquitin-protein ligases, including NEDD4 and ITCH, and consequently modulates the stability of their targets. As a result, controls many cellular processes. Prevents chronic T-helper cell-mediated inflammation by activating ITCH and thus controlling JUNB degradation (By similarity). Promotes pancreatic beta cell death through degradation of JUNB and inhibition of the unfolded protein response, leading to reduction of insulin secretion (PubMed:26319551). Restricts the production of proinflammatory cytokines in effector Th17 T-cells by promoting ITCH-mediated ubiquitination and degradation of RORC (By similarity). Together with NDFIP2, 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). Regulates peripheral T-cell tolerance to self and foreign antigens, forcing the exit of naive CD4+ T-cells from the cell cycle before they become effector T-cells (By similarity). Negatively regulates RLR-mediated antiviral response by promoting SMURF1-mediated ubiquitination and subsequent degradation of MAVS (PubMed:23087404). 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 where it mediates KCNH2 degradation (PubMed:26363003). In cortical neurons, mediates the ubiquitination of the divalent metal transporter SLC11A2/DMT1 by NEDD4L, leading to its down- regulation and protection of the cells from cobalt and iron toxicity (PubMed:19706893). Important for normal development of dendrites and dendritic spines in cortex (By similarity). Enhances the ubiquitination of BRAT1 mediated by: NEDD4, NEDD4L and ITCH and is required for the nuclear localization of ubiquitinated BRAT1 (PubMed:25631046). Enhances the ITCH-mediated ubiquitination of MAP3K7 by recruiting E2 ubiquitin-conjugating enzyme UBE2L3 to ITCH (By similarity). Modulates EGFR signaling through multiple pathways. In particular, may regulate the ratio of AKT1-to-MAPK8 signaling in response to EGF, acting on AKT1 probably through PTEN destabilization and on MAPK8 through ITCH-dependent MAP2K4 inactivation. As a result, may control cell growth rate (PubMed:20534535). Inhibits cell proliferation by promoting PTEN nuclear localization and changing its signaling specificity (PubMed:25801959). {ECO:0000250|UniProtKB:Q8R0W6, ECO:0000269|PubMed:19343052, ECO:0000269|PubMed:19706893, ECO:0000269|PubMed:20534535, ECO:0000269|PubMed:23087404, ECO:0000269|PubMed:25631046, ECO:0000269|PubMed:25801959, ECO:0000269|PubMed:26319551, ECO:0000269|PubMed:26363003}.;

Recessive Scores

pRec
0.124

Intolerance Scores

LoFtool
0.232
RVIS EVS
-0.16
RVIS percentile EVS
41.25

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.731

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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