PDXK

pyridoxal kinase

Basic information

Region (hg38): 21:43719094-43762307

Previous symbols: [ "C21orf97", "C21orf124" ]

Links

ENSG00000160209 ∙ NCBI:8566 ∙ OMIM:179020 ∙ HGNC:8819 ∙ Uniprot:O00764 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neuropathy, hereditary motor and sensory, type VIc, with optic atrophy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hereditary motor and sensory neuropathy, type VIC, with optic atrophy (Charcot-Marie-Tooth disease, type 6C)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	31187503

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDXK gene.

• PDXK-related disorder (1 variants)
• not provided (1 variants)
• Neuropathy, hereditary motor and sensory, type VIc, with optic atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDXK 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				5	3	8
missense	1	1	12	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region					1	1
non coding			1		23	24
Total	2	1	13	8	26

Highest pathogenic variant AF is 0.0000263

Variants in PDXK

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

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

Position	Type	Phenotype	Significance	ClinVar
21-43719132-A-G			Benign (May 22, 2021)
21-43733870-A-G			Benign (May 13, 2021)
21-43734091-C-T		not specified	Uncertain significance (Jul 02, 2024)
21-43734104-C-G			Likely benign (Jul 01, 2022)
21-43734121-C-T		not specified	Uncertain significance (Aug 01, 2024)
21-43734131-G-A		PDXK-related disorder	Likely benign (Jul 23, 2024)
21-43734263-C-T			Benign (May 13, 2021)
21-43734293-CAG-C			Benign (May 14, 2021)
21-43737181-C-T			Likely benign (Oct 01, 2024)
21-43737288-G-A			Likely benign (May 01, 2024)
21-43741465-G-A			Benign (May 14, 2021)
21-43741551-A-G		PDXK-related disorder	Benign (May 13, 2021)
21-43741552-T-C		PDXK-related disorder	Benign (Dec 26, 2019)
21-43741567-C-T		PDXK-related disorder	Uncertain significance (Nov 15, 2023)
21-43741672-G-A		not specified	Uncertain significance (Jun 02, 2023)
21-43741744-A-G		not specified	Likely benign (Dec 13, 2021)
21-43741749-T-A		Neuropathy, hereditary motor and sensory, type VIc, with optic atrophy	Likely pathogenic (Sep 30, 2020)
21-43741969-T-C			Benign (May 14, 2021)
21-43743730-C-T			Uncertain significance (Jul 01, 2024)
21-43743731-G-A		PDXK-related disorder	Likely benign (Apr 01, 2024)
21-43743765-A-G		not specified	Uncertain significance (Jul 13, 2021)
21-43743833-T-G		Neuropathy, hereditary motor and sensory, type VIc, with optic atrophy	Benign (Sep 05, 2021)
21-43743885-G-A			Benign (May 14, 2021)
21-43743986-G-T			Benign (May 15, 2021)
21-43746121-C-T		Neuropathy, hereditary motor and sensory, type VIc, with optic atrophy	Likely benign (Nov 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDXK	protein_coding	protein_coding	ENST00000291565	11	43214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.749	0.251	125667	0	5	125672	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	118	191	0.619	0.0000116	2043
Missense in Polyphen		20	55.608	0.35966		694
Synonymous	0.813	72	81.3	0.885	0.00000563	586
Loss of Function	3.24	3	17.7	0.169	7.53e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000999	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
• Pathway: Vitamin B6 metabolism - Homo sapiens (human);Hypophosphatasia;Vitamin B6 Metabolism;Neutrophil degranulation;Innate Immune System;Immune System;Metabolism;Vitamins B6 activation to pyridoxal phosphate;Metabolism of water-soluble vitamins and cofactors;pyridoxal 5,-phosphate salvage;Metabolism of vitamins and cofactors;Vitamin B6 metabolism (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.300
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.0955
• hipred: Y
• hipred_score: 0.728
• ghis: 0.584

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdxk
• 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)

Gene ontology

• Biological process: cell population proliferation;pyridoxal 5'-phosphate salvage;phosphorylation;vitamin B6 metabolic process;pyridoxal phosphate biosynthetic process;neutrophil degranulation
• Cellular component: extracellular region;nucleus;nucleoplasm;cytosol;secretory granule lumen;specific granule lumen;extracellular exosome
• Molecular function: magnesium ion binding;ATP binding;zinc ion binding;pyridoxal kinase activity;pyridoxal phosphate binding;potassium ion binding;sodium ion binding;lithium ion binding;protein homodimerization activity