GMCL1

germ cell-less 1, spermatogenesis associated, the group of BTB domain containing

Basic information

Region (hg38): 2:69829659-69881384

Links

ENSG00000087338 ∙ NCBI:64395 ∙ OMIM:618627 ∙ HGNC:23843 ∙ Uniprot:Q96IK5 ∙ 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 GMCL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMCL1 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	15	0	2

Variants in GMCL1

This is a list of pathogenic ClinVar variants found in the GMCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-69829930-G-A		not specified	Uncertain significance (Oct 03, 2023)
2-69830034-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-69830092-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-69830123-G-C		not specified	Uncertain significance (May 24, 2023)
2-69841026-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-69843188-A-G		not specified	Uncertain significance (Sep 27, 2022)
2-69844206-T-C			Benign (Dec 31, 2019)
2-69847575-C-T		not specified	Uncertain significance (May 01, 2024)
2-69854858-G-A		not specified	Uncertain significance (May 31, 2023)
2-69864971-G-A		not specified	Uncertain significance (May 18, 2022)
2-69869729-G-A		not specified	Uncertain significance (Feb 05, 2024)
2-69869761-C-G		not specified	Uncertain significance (Dec 15, 2023)
2-69869818-T-G		not specified	Uncertain significance (Oct 20, 2021)
2-69869846-G-A			Benign (May 04, 2018)
2-69871767-A-G		not specified	Uncertain significance (Mar 17, 2023)
2-69871782-A-T		not specified	Uncertain significance (May 09, 2023)
2-69871804-A-G		not specified	Uncertain significance (Jan 02, 2024)
2-69878979-A-G		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMCL1	protein_coding	protein_coding	ENST00000282570	14	51755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.57e-7	0.997	125702	0	44	125746	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	212	268	0.792	0.0000128	3366
Missense in Polyphen		31	53.742	0.57683		718
Synonymous	-0.678	100	91.7	1.09	0.00000424	914
Loss of Function	2.67	16	32.4	0.494	0.00000158	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00175	0.00103
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000136	0.000132
Middle Eastern	0.00175	0.00103
South Asian	0.000142	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible function in spermatogenesis. Enhances the degradation of MDM2 and increases the amount of p53 probably by modulating the nucleocytoplasmic transport (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.826
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.454
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmcl1
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: nuclear matrix
• Molecular function: protein binding;identical protein binding