GMFG

glia maturation factor gamma

Basic information

Region (hg38): 19:39328353-39342372

Links

ENSG00000130755 ∙ NCBI:9535 ∙ OMIM:604104 ∙ HGNC:4374 ∙ Uniprot:O60234 ∙ 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 GMFG gene.

• not_specified (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMFG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004877.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMFG	protein_coding	protein_coding	ENST00000597595	7	14020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-8	0.105	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.180	79	83.6	0.945	0.00000469	942
Missense in Polyphen		25	29.308	0.85301		307
Synonymous	-0.460	33	29.8	1.11	0.00000174	243
Loss of Function	-0.0876	12	11.7	1.03	6.68e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000699	0.000697
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.00	0.00
South Asian	0.00105	0.00105
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.781
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.544
• hipred: N
• hipred_score: 0.279
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.315

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmfg

Zebrafish Information Network

• Gene name: gmfg
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: protein phosphorylation;negative regulation of protein kinase activity;regulation of signaling receptor activity;negative regulation of Arp2/3 complex-mediated actin nucleation;positive regulation of catalytic activity;neutrophil degranulation;actin filament debranching;regulation of actin cytoskeleton reorganization
• Cellular component: extracellular region;actin cortical patch;secretory granule lumen;ficolin-1-rich granule lumen
• Molecular function: actin binding;protein kinase inhibitor activity;enzyme activator activity;growth factor activity;Arp2/3 complex binding