GGN

gametogenetin

Basic information

Region (hg38): 19:38384266-38388082

Links

ENSG00000179168 ∙ NCBI:199720 ∙ OMIM:609966 ∙ HGNC:18869 ∙ Uniprot:Q86UU5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 69 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 69	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	31985809; 33108537

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGN 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				4		4
missense			36	4	7	47
nonsense				1		1
start loss						0
frameshift						0
inframe indel			1	1	1	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	10	8

Variants in GGN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-38384432-G-A		GGN-related disorder	Benign/Likely benign (Dec 01, 2023)
19-38384432-G-C			Benign (Dec 31, 2019)
19-38384525-T-C		not specified	Uncertain significance (Sep 26, 2023)
19-38385436-C-T		not specified	Uncertain significance (May 31, 2023)
19-38385449-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-38385557-C-A		not specified	Uncertain significance (Apr 26, 2024)
19-38385619-G-A		not specified	Uncertain significance (May 16, 2024)
19-38385622-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-38385623-C-T			Benign (Dec 31, 2019)
19-38385650-T-C		not specified	Uncertain significance (Aug 16, 2022)
19-38385692-G-T		not specified	Uncertain significance (Jan 10, 2023)
19-38385740-A-G		not specified	Uncertain significance (Aug 10, 2023)
19-38385765-A-AGCCGGGGATGGGGCCGGGGCCGGG			Benign (Dec 31, 2019)
19-38385791-C-T		GGN-related disorder	Likely benign (May 31, 2023)
19-38385820-G-T		not specified	Uncertain significance (Aug 04, 2021)
19-38385847-T-C		not specified	Uncertain significance (Dec 06, 2021)
19-38385863-G-C		not specified	Uncertain significance (Jan 25, 2024)
19-38385910-G-A		not specified	Uncertain significance (May 08, 2023)
19-38385916-AGTGTGGGCGGCG-A			Uncertain significance (Jan 01, 2024)
19-38385975-C-T		not specified	Likely benign (Feb 17, 2024)
19-38385990-GC-G		Spermatogenic failure 69	Pathogenic (Apr 05, 2022)
19-38386048-C-T			Benign (Dec 31, 2019)
19-38386085-G-A			Benign/Likely benign (May 01, 2024)
19-38386118-C-T			Benign (Dec 31, 2019)
19-38386129-C-T		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGN	protein_coding	protein_coding	ENST00000334928	2	3818

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00186	0.977	125686	0	40	125726	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.395	399	422	0.946	0.0000305	3912
Missense in Polyphen		49	61.421	0.79777		523
Synonymous	2.79	159	210	0.755	0.0000167	1581
Loss of Function	2.03	7	15.7	0.447	9.17e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000270
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000168	0.000163
Finnish	0.000144	0.000139
European (Non-Finnish)	0.000171	0.000149
Middle Eastern	0.000168	0.000163
South Asian	0.000236	0.000229
Other	0.000194	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in spermatogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Haploinsufficiency Scores

• pHI: 0.0553
• hipred: N
• hipred_score: 0.254
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ggn
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: double-strand break repair;gamete generation;spermatogenesis;embryo implantation;protein localization;cell differentiation
• Cellular component: nucleolus;perinuclear region of cytoplasm
• Molecular function: protein binding;ubiquitin protein ligase binding;protein dimerization activity