GMNC

geminin coiled-coil domain containing

Basic information

Region (hg38): 3:190852737-190892429

Links

ENSG00000205835 ∙ NCBI:647309 ∙ OMIM:614448 ∙ HGNC:40049 ∙ Uniprot:A6NCL1 ∙ 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 GMNC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMNC 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in GMNC

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

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

Position	Type	Phenotype	Significance	ClinVar
3-190855327-A-G		not specified	Uncertain significance (Dec 13, 2022)
3-190855410-G-A		not specified	Uncertain significance (May 02, 2023)
3-190855508-G-T		not specified	Uncertain significance (Oct 12, 2022)
3-190855560-C-A		not specified	Uncertain significance (Nov 18, 2022)
3-190855572-A-G		not specified	Uncertain significance (Mar 16, 2024)
3-190855575-G-A		not specified	Uncertain significance (Jul 20, 2022)
3-190855841-T-G		not specified	Uncertain significance (Aug 20, 2023)
3-190855873-A-G		not specified	Uncertain significance (Jun 01, 2022)
3-190857784-T-G		not specified	Uncertain significance (Mar 31, 2024)
3-190857811-A-G		not specified	Uncertain significance (Oct 02, 2023)
3-190857824-G-C		not specified	Uncertain significance (Jan 10, 2022)
3-190857862-G-A		not specified	Uncertain significance (Apr 20, 2024)
3-190857871-T-A		not specified	Uncertain significance (May 09, 2023)
3-190857872-C-T		not specified	Uncertain significance (Jun 21, 2023)
3-190857883-A-G		not specified	Uncertain significance (Feb 03, 2022)
3-190858935-T-C		not specified	Uncertain significance (Oct 13, 2023)
3-190858939-T-C		not specified	Uncertain significance (Jan 24, 2023)
3-190858990-G-A		not specified	Uncertain significance (May 01, 2024)
3-190858992-G-A		not specified	Uncertain significance (Oct 10, 2023)
3-190859005-C-T		not specified	Uncertain significance (Jan 11, 2023)
3-190860720-C-T		not specified	Uncertain significance (May 12, 2024)
3-190860780-C-T		not specified	Uncertain significance (Nov 22, 2023)
3-190860785-G-A		not specified	Uncertain significance (Jun 17, 2024)
3-190860800-G-T		not specified	Uncertain significance (Nov 06, 2023)
3-190860801-G-A		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMNC	protein_coding	protein_coding	ENST00000442080	5	39553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.447	0.552	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.534	149	169	0.884	0.00000826	2183
Missense in Polyphen		57	64.293	0.88657		861
Synonymous	1.77	49	67.5	0.726	0.00000380	636
Loss of Function	2.76	3	14.2	0.211	6.47e-7	190

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: Regulator of DNA replication. Promotes initiation of chromosomal DNA replication by mediating TOPBP1- and CDK2- dependent recruitment of CDC45L onto replication origins (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.84

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmnc
• Phenotype: cellular phenotype; growth/size/body region 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); respiratory system phenotype

Zebrafish Information Network

• Gene name: gmnc
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: lacks parts or has fewer parts of type

Gene ontology

• Biological process: DNA replication initiation;cell cycle;cell population proliferation;cilium assembly
• Cellular component: nucleus
• Molecular function: chromatin binding