IDNK

protein-coding

IDNK gluconokinase

Gene summary

Predicted to enable gluconokinase activity. Predicted to be involved in carbohydrate metabolic process. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf103

MANE transcript

NM_001001551.4

Inheritance

—

ClinVar variants

U:38B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr9:83,623,049-83,644,130

External References & Databases

Ensembl (ENSG00000148057)

Transcript & Mutation Effects

hg38 • Region Span ~21.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IDNK variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001551.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			36 clinvar	2 clinvar		38
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	38	6	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001551.4	RefSeq	NP_001001551.2	5	MANE Select
ENST00000376419.5	Ensembl	ENSP00000365601.4	5	MANE Select
NM_001256915.2	RefSeq	NP_001243844.1	3	Standard
NM_001351535.2	RefSeq	NP_001338464.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pentose phosphate pathway - Homo sapiens (human)

Biological Process

biological_process
phosphorylation
D-gluconate catabolic process

Molecular Function

molecular_function
ATP binding
gluconokinase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376419
Coding exons: 5
Length: 21082
Individuals with no LoFs: 125726
Homozygous LoFs: 1
Heterozygous LoFs: 21
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.368	91	101	0.897	0.00000565	1194
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00036	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.139

Intolerance Scores

RVIS EVS: 0.64
RVIS percentile EVS: 83.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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