NSMF NMDA receptor synaptonuclear signaling and neuronal migration factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: NSMFprovided by HGNC
Official Full Name: NMDA receptor synaptonuclear signaling and neuronal migration factorprovided by HGNC
Primary source: HGNC:HGNC:29843
See related: Ensembl:ENSG00000165802 MIM:608137; AllianceGenome:HGNC:29843
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HH9; NELF
Summary: The protein encoded by this gene is involved in guidance of olfactory axon projections and migration of luteinizing hormone-releasing hormone neurons. Defects in this gene are a cause of idiopathic hypogonadotropic hypogonadism (IHH). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
Expression: Broad expression in brain (RPKM 43.0), kidney (RPKM 13.5) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (137447570..137459334, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (149698122..149709468, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (140342022..140353786, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NELF and PAF1C complexes are core transcriptional machineries controlling colon cancer stemness.
Title: NELF and PAF1C complexes are core transcriptional machineries controlling colon cancer stemness.
NSMF promotes the replication stress-induced DNA damage response for genome maintenance.
Title: NSMF promotes the replication stress-induced DNA damage response for genome maintenance.
These findings suggest a role for NELF in the regulation of the JAK/STAT signaling pathway, which have important functions in GnRH neurons.
Title: JAK/STAT signaling pathway gene expression is reduced following Nelf knockdown in GnRH neurons.
The nuclear and non-nuclear NELF variant transcripts and proteins were identified, explaining variable NELF cellular localization.
Title: Differential expression of nasal embryonic LHRH factor (NELF) variants in immortalized GnRH neuronal cell lines.
a model in which NELF recruits Pcf11 and NCoR1-GPS2-HDAC3 to paused RNAP II, reinforcing repression of HIV transcription and establishing a critical checkpoint for HIV transcription and latency.
Title: Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription.
NELF is associated with normosmic idiopathic hypogonadotropic hypogonadism and Kallmann syndrome, either singly or in combination with a mutation in another gene.
Title: Nasal embryonic LHRH factor (NELF) mutations in patients with normosmic hypogonadotropic hypogonadism and Kallmann syndrome.
our findings implicate NELF as a nuclear protein involved in the developmental function of the reproductive axis.
Title: NELF is a nuclear protein involved in hypothalamic GnRH neuronal migration.
Observational study of gene-disease association. (HuGE Navigator)
Title: Screening of autosomal gene deletions in patients with hypogonadotropic hypogonadism using multiplex ligation-dependent probe amplification: detection of a hemizygosis for the fibroblast growth factor receptor 1.
12% of Kallman syndrome males have KAL1 deletions, but intragenic deletions of the FGFR1, GNRH1, GNRHR, GPR54 and NELF genes are uncommon in Idiopathic hypogonadotropic hypogonadism/Kallman syndrome.
Title: The prevalence of intragenic deletions in patients with idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hypogonadotropic hypogonadism 9 with or without anosmia MedGen: C3553842 OMIM: 614838 GeneReviews: Isolated Gonadotropin-Releasing Hormone (GnRH) Deficiency	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NELF_1409 (e-PCR)
- UniSTS:277528

NELF_v455 (e-PCR)
- UniSTS:277528

IB1002 (e-PCR)
- UniSTS:74109

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium-dependent protein binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in cellular response to amino acid stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to electrical stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to gonadotropin stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neuron migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein dephosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of dendrite morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuron apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in apical dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in cortical cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
part_of euchromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear envelope	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear matrix	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perikaryon	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	ISS Inferred from Sequence or Structural Similarity more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: NMDA receptor synaptonuclear signaling and neuronal migration factor

Names: nasal embryonic LHRH factor; nasal embryonic luteinizing hormone-releasing hormone factor

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_021362.1 RefSeqGene

Range

5001..16765

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001130969.3 → NP_001124441.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform a

See identical proteins and their annotated locations for NP_001124441.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AL365502

Consensus CDS

CCDS48069.1

UniProtKB/Swiss-Prot

Q2TB96, Q6X4V7, Q6X4V8, Q6X4V9, Q6X4W1, Q8N2M2, Q96SY1, Q9NPM4, Q9NPP3, Q9NPS3

Related

ENSP00000360530.3, ENST00000371475.9
NM_001130970.2 → NP_001124442.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform c

See identical proteins and their annotated locations for NP_001124442.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AW072125, AY255130, BM023184, CN306732

Consensus CDS

CCDS48068.1

UniProtKB/Swiss-Prot

Q6X4W1

Related

ENSP00000412007.1, ENST00000437259.5
NM_001130971.2 → NP_001124443.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform d

See identical proteins and their annotated locations for NP_001124443.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AW072125, AY255128, BC110498, BM023184, CN306732

Consensus CDS

CCDS48067.1

UniProtKB/Swiss-Prot

Q6X4W1

Related

ENSP00000360529.3, ENST00000371474.7
NM_001178064.2 → NP_001171535.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform e

See identical proteins and their annotated locations for NP_001171535.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (e) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AW072125, AY255131, BM023184, CN306732

Consensus CDS

CCDS55357.1

UniProtKB/Swiss-Prot

Q6X4W1

Related

ENSP00000360528.3, ENST00000371473.7
NM_015537.5 → NP_056352.3 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform b

See identical proteins and their annotated locations for NP_056352.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AW072125, AY255128, BC072412, BM023184, CN306732

Consensus CDS

CCDS7044.1

UniProtKB/Swiss-Prot

Q6X4W1

Related

ENSP00000265663.7, ENST00000265663.12

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

137447570..137459334 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005266062.6 → XP_005266119.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X3
XM_005266061.6 → XP_005266118.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X1

See identical proteins and their annotated locations for XP_005266118.1
XM_011518496.4 → XP_011516798.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X2
XM_011518497.3 → XP_011516799.2 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X4
XM_017014597.3 → XP_016870086.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

149698122..149709468 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054362656.1 → XP_054218631.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X3
XM_054362654.1 → XP_054218629.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X1
XM_054362655.1 → XP_054218630.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X2
XM_054362658.1 → XP_054218633.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X5
XM_054362657.1 → XP_054218632.1 NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X4