GNRH2

gonadotropin releasing hormone 2, the group of Neuropeptides

Basic information

Region (hg38): 20:3043621-3045747

Links

ENSG00000125787 ∙ NCBI:2797 ∙ OMIM:602352 ∙ HGNC:4420 ∙ Uniprot:O43555 ∙ 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 GNRH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNRH2 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					1	1
missense			3	3	1	7
nonsense						0
start loss						0
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	4	3

Variants in GNRH2

This is a list of pathogenic ClinVar variants found in the GNRH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3044419-C-T		not specified	Uncertain significance (Jun 03, 2024)
20-3044467-T-C		not specified	Likely benign (Nov 01, 2022)
20-3044526-C-T		not specified	Uncertain significance (Jun 18, 2024)
20-3044684-G-A			Benign (Dec 31, 2019)
20-3044743-C-T			Benign (Dec 28, 2017)
20-3044786-A-G		not specified	Uncertain significance (Jul 06, 2021)
20-3044787-C-T		not specified	Likely benign (Jan 10, 2023)
20-3045686-A-G		not specified	Uncertain significance (Jan 04, 2022)
20-3045698-G-A		not specified	Uncertain significance (Sep 06, 2022)
20-3045699-A-C		not specified	Likely benign (Jul 06, 2022)
20-3045699-A-AGCCCC			Benign (Dec 19, 2019)
20-3045705-G-GCCCCT			Likely benign (Feb 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNRH2	protein_coding	protein_coding	ENST00000245983	3	2126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-7	0.0625	125582	0	6	125588	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.389	76	67.0	1.13	0.00000342	730
Missense in Polyphen		30	29.858	1.0048		338
Synonymous	1.40	20	29.7	0.672	0.00000147	271
Loss of Function	-0.984	9	6.33	1.42	4.40e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.000191	0.000185
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000557	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates the secretion of gonadotropins; it stimulates the secretion of both luteinizing and follicle-stimulating hormones.
• Pathway: GnRH signaling pathway - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Hormone ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.235

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.0296
• hipred: N
• hipred_score: 0.123
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0177

Gene Damage Prediction

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

Gene ontology

• Biological process: reproduction;signal transduction;G protein-coupled receptor signaling pathway;multicellular organism development;regulation of signaling receptor activity
• Cellular component: extracellular region;extracellular space
• Molecular function: hormone activity;gonadotropin hormone-releasing hormone activity;gonadotropin-releasing hormone receptor binding