GFOD2

glucose-fructose oxidoreductase domain containing 2

Basic information

Region (hg38): 16:67674531-67719339

Links

ENSG00000141098 ∙ NCBI:81577 ∙ OMIM:619933 ∙ HGNC:28159 ∙ Uniprot:Q3B7J2 ∙ 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 GFOD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GFOD2 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in GFOD2

This is a list of pathogenic ClinVar variants found in the GFOD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67675177-G-A		not specified	Uncertain significance (Sep 07, 2022)
16-67675206-C-A		not specified	Uncertain significance (Dec 02, 2024)
16-67675213-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-67675298-C-T		not specified	Uncertain significance (Jan 03, 2024)
16-67675315-G-A		not specified	Uncertain significance (Dec 05, 2022)
16-67675342-C-T		not specified	Uncertain significance (Nov 15, 2024)
16-67675346-C-T		not specified	Uncertain significance (Nov 16, 2024)
16-67675369-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-67675387-T-C		not specified	Uncertain significance (Dec 16, 2023)
16-67675414-G-A		not specified	Uncertain significance (Jan 10, 2023)
16-67675448-C-T		not specified	Uncertain significance (May 09, 2023)
16-67675450-C-A		not specified	Uncertain significance (Aug 10, 2024)
16-67675489-G-A		not specified	Uncertain significance (Jun 08, 2022)
16-67675538-G-A		not specified	Uncertain significance (Nov 11, 2024)
16-67675577-C-T		not specified	Uncertain significance (Jan 22, 2024)
16-67675645-C-T		not specified	Uncertain significance (Dec 15, 2022)
16-67675664-C-T		not specified	Uncertain significance (Dec 27, 2022)
16-67675679-G-A		not specified	Uncertain significance (Sep 14, 2021)
16-67675730-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-67675777-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-67675816-C-G		not specified	Uncertain significance (Mar 22, 2022)
16-67675874-T-A		not specified	Uncertain significance (Aug 30, 2021)
16-67675892-A-G		not specified	Uncertain significance (Feb 27, 2024)
16-67675899-C-T			Likely benign (Jun 01, 2022)
16-67675919-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GFOD2	protein_coding	protein_coding	ENST00000268797	2	44891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0466	0.931	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	216	262	0.824	0.0000174	2487
Missense in Polyphen		69	89.205	0.7735		867
Synonymous	0.858	104	116	0.899	0.00000813	831
Loss of Function	1.99	4	11.2	0.358	6.48e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes matrix assembly. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.565
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.459
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.365

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gfod2

Gene ontology

• Biological process: extracellular matrix organization;oxidation-reduction process
• Cellular component: extracellular matrix
• Molecular function: oxidoreductase activity