NPVF

neuropeptide VF precursor, the group of Neuropeptides

Basic information

Region (hg38): 7:25224570-25228486

Previous symbols: [ "C7orf9" ]

Links

ENSG00000105954 ∙ NCBI:64111 ∙ OMIM:616984 ∙ HGNC:13782 ∙ Uniprot:Q9HCQ7 ∙ 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 NPVF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPVF 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in NPVF

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

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

Position	Type	Phenotype	Significance	ClinVar
7-25225145-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-25226642-C-A		not specified	Uncertain significance (Sep 24, 2024)
7-25226642-C-T		not specified	Uncertain significance (Feb 20, 2025)
7-25226645-G-A		not specified	Uncertain significance (Sep 01, 2021)
7-25226672-T-A		not specified	Uncertain significance (Aug 03, 2022)
7-25226677-G-A		not specified	Uncertain significance (Jan 19, 2024)
7-25226681-A-G		not specified	Uncertain significance (Sep 11, 2024)
7-25226699-A-G		not specified	Uncertain significance (Apr 14, 2022)
7-25226702-G-A		not specified	Uncertain significance (Apr 12, 2024)
7-25226730-A-T		not specified	Uncertain significance (Jan 03, 2024)
7-25226731-C-T		not specified	Uncertain significance (Nov 12, 2021)
7-25226762-T-C		not specified	Uncertain significance (Jun 22, 2021)
7-25226767-C-T		not specified	Uncertain significance (Feb 01, 2025)
7-25226788-T-C		not specified	Uncertain significance (May 08, 2024)
7-25226797-C-T		not specified	Likely benign (Mar 20, 2024)
7-25226798-G-A		not specified	Uncertain significance (Oct 17, 2024)
7-25226843-G-T		not specified	Uncertain significance (Jan 02, 2025)
7-25226844-G-T		not specified	Uncertain significance (Dec 14, 2021)
7-25226975-C-T		not specified	Uncertain significance (Jan 23, 2025)
7-25226997-G-C		not specified	Uncertain significance (Feb 10, 2022)
7-25227023-T-C		not specified	Uncertain significance (Feb 01, 2025)
7-25228318-T-C		not specified	Uncertain significance (Sep 12, 2023)
7-25228342-G-A		not specified	Uncertain significance (Oct 22, 2024)
7-25228393-G-A		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPVF	protein_coding	protein_coding	ENST00000222674	3	3917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000104	0.375	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.603	114	97.3	1.17	0.00000476	1286
Missense in Polyphen		15	17.31	0.86654		261
Synonymous	0.392	34	37.0	0.918	0.00000195	355
Loss of Function	0.0446	6	6.12	0.981	2.53e-7	100

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neuropeptide RFRP-1 acts as a potent negative regulator of gonadotropin synthesis and secretion. Neuropeptides NPSF and NPVF efficiently inhibit forskolin-induced production of cAMP, but RFRP-2 shows no inhibitory activity. Neuropeptide RFRP-1 induces secretion of prolactin in rats. Neuropeptide NPVF blocks morphine- induced analgesia. {ECO:0000269|PubMed:11025660, ECO:0000269|PubMed:20027225}.

Recessive Scores

• pRec: 0.0894

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00730

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npvf

Zebrafish Information Network

• Gene name: npvf
• Affected structure: swimming behavior
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: neuropeptide signaling pathway;negative regulation of gonadotropin secretion
• Cellular component: extracellular region