IDNK

IDNK gluconokinase

Basic information

Region (hg38): 9:83623049-83644130

Previous symbols: [ "C9orf103" ]

Links

ENSG00000148057 ∙ NCBI:414328 ∙ OMIM:611343 ∙ HGNC:31367 ∙ Uniprot:Q5T6J7 ∙ 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 IDNK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDNK 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			14	1		15
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in IDNK

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

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

Position	Type	Phenotype	Significance	ClinVar
9-83623182-C-G		not specified	Uncertain significance (Feb 28, 2023)
9-83623196-G-C		not specified	Uncertain significance (Jun 07, 2024)
9-83623210-C-A		not specified	Uncertain significance (Nov 09, 2024)
9-83623215-C-T		not specified	Uncertain significance (May 15, 2024)
9-83628194-G-A		not specified	Uncertain significance (Feb 21, 2025)
9-83628917-A-G		not specified	Likely benign (Mar 14, 2025)
9-83628934-G-C		not specified	Uncertain significance (Jan 18, 2025)
9-83643449-G-A		not specified	Likely benign (Jan 10, 2025)
9-83643482-C-T		not specified	Likely benign (Jul 28, 2021)
9-83643488-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-83643530-G-A		not specified	Uncertain significance (Jan 08, 2025)
9-83643536-A-G		not specified	Uncertain significance (Dec 01, 2022)
9-83643598-T-C		not specified	Uncertain significance (Apr 15, 2024)
9-83643610-T-C		not specified	Uncertain significance (Sep 27, 2021)
9-83643616-C-T		not specified	Uncertain significance (Sep 03, 2024)
9-83643622-C-T		not specified	Uncertain significance (May 18, 2023)
9-83643634-G-A		not specified	Uncertain significance (Jan 08, 2024)
9-83643638-A-G		not specified	Uncertain significance (Mar 27, 2023)
9-83643676-A-T		not specified	Uncertain significance (Dec 08, 2023)
9-83643737-CAG-C			Likely benign (Sep 19, 2017)
9-83643742-A-G		not specified	Uncertain significance (Dec 25, 2024)
9-83643742-A-T		not specified	Uncertain significance (Dec 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IDNK	protein_coding	protein_coding	ENST00000376419	5	21082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.393	0.598	125726	1	21	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.368	91	101	0.897	0.00000565	1194
Missense in Polyphen		29	39.321	0.73753		452
Synonymous	0.0442	40	40.4	0.991	0.00000244	367
Loss of Function	2.21	2	9.25	0.216	4.55e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000359	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Pentose phosphate pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.208
• ghis: 0.379

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Idnk
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: biological_process;phosphorylation;D-gluconate catabolic process
• Molecular function: molecular_function;ATP binding;gluconokinase activity