NENF

neudesin neurotrophic factor, the group of Membrane associated progesterone receptor family

Basic information

Region (hg38): 1:212432920-212446379

Links

ENSG00000117691 ∙ NCBI:29937 ∙ OMIM:611874 ∙ HGNC:30384 ∙ Uniprot:Q9UMX5 ∙ 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 NENF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NENF 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in NENF

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

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

Position	Type	Phenotype	Significance	ClinVar
1-212432954-C-G		not specified	Uncertain significance (Mar 03, 2025)
1-212432965-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-212432974-C-T		not specified	Uncertain significance (Dec 11, 2024)
1-212433031-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-212433056-C-A		not specified	Uncertain significance (Feb 03, 2022)
1-212433089-A-C		not specified	Uncertain significance (Nov 18, 2022)
1-212444351-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-212444357-C-T		not specified	Uncertain significance (Oct 30, 2024)
1-212444375-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-212444386-T-A		not specified	Uncertain significance (May 31, 2023)
1-212444395-G-A		not specified	Uncertain significance (Jul 19, 2023)
1-212444426-A-G		not specified	Uncertain significance (Jan 20, 2025)
1-212444438-A-G		not specified	Uncertain significance (Apr 19, 2024)
1-212445882-T-C		not specified	Uncertain significance (Dec 01, 2022)
1-212445915-C-G		not specified	Uncertain significance (Mar 08, 2025)
1-212445920-C-T		not specified	Uncertain significance (May 09, 2023)
1-212445921-G-A		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NENF	protein_coding	protein_coding	ENST00000366988	4	13486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0216	0.772	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	62	64.6	0.960	0.00000354	1080
Missense in Polyphen		23	25.753	0.89309		346
Synonymous	-0.351	29	26.7	1.09	0.00000154	389
Loss of Function	0.901	3	5.22	0.574	3.06e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000430	0.000429
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000717	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a neurotrophic factor in postnatal mature neurons enhancing neuronal survival. Promotes cell proliferation and neurogenesis in undifferentiated neural pro-genitor cells at the embryonic stage and inhibits differentiation of astrocyte. Its neurotrophic activity is exerted via MAPK1/ERK2, MAPK3/ERK1 and AKT1/AKT pathways. Neurotrophic activity is enhanced by binding to heme. Acts also as an anorexigenic neurotrophic factor that contributes to energy balance (By similarity). Plays a role in the human tumorigenesis (PubMed:22748190). {ECO:0000250|UniProtKB:Q9CQ45, ECO:0000269|PubMed:22748190}.

Recessive Scores

• pRec: 0.119

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.352
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.334

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nenf
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of signaling receptor activity;negative regulation of appetite;positive regulation of MAPK cascade
• Cellular component: extracellular space;nucleus;nucleoplasm
• Molecular function: growth factor activity;metal ion binding