NME9

NME/NM23 family member 9, the group of NME/NM23 family|Thioredoxin domain containing

Basic information

Region (hg38): 3:138261436-138329886

Previous symbols: [ "TXNDC6" ]

Links

ENSG00000181322 ∙ NCBI:347736 ∙ OMIM:618584 ∙ HGNC:21343 ∙ Uniprot:Q86XW9 ∙ 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 NME9 gene.

• Inborn genetic diseases (14 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NME9 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			9	3		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	12	3	1

Variants in NME9

This is a list of pathogenic ClinVar variants found in the NME9 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-138270061-G-A		not specified	Uncertain significance (Aug 08, 2022)
3-138273015-A-G		not specified	Uncertain significance (Oct 17, 2023)
3-138274467-A-G		not specified	Uncertain significance (Sep 20, 2023)
3-138295866-A-G		not specified	Uncertain significance (Feb 11, 2022)
3-138295868-G-C			Uncertain significance (Mar 16, 2021)
3-138303516-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-138303590-C-T		not specified	Likely benign (Feb 16, 2023)
3-138303603-C-T		not specified	Uncertain significance (Jul 27, 2022)
3-138303627-C-A		not specified	Uncertain significance (Jun 02, 2023)
3-138304882-T-C		not specified	Uncertain significance (Oct 03, 2023)
3-138304900-T-C		not specified	Uncertain significance (Jul 20, 2021)
3-138304910-G-A		not specified	Likely benign (Aug 21, 2023)
3-138304922-C-T		not specified	Likely benign (Apr 07, 2022)
3-138314339-C-T		not specified	Benign (Mar 29, 2016)
3-138314362-C-T		not specified	Uncertain significance (May 03, 2023)
3-138318167-G-T		not specified	Uncertain significance (Oct 26, 2021)
3-138318204-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-138318215-T-C		not specified	Uncertain significance (Aug 02, 2022)
3-138319489-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-138319575-T-G		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NME9	protein_coding	protein_coding	ENST00000383180	9	68450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.89e-9	0.281	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.961	116	149	0.779	0.00000780	1741
Missense in Polyphen		34	51.848	0.65576		648
Synonymous	-1.40	69	55.7	1.24	0.00000312	484
Loss of Function	0.631	14	16.8	0.834	9.68e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000673	0.000673
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000328	0.000299
Middle Eastern	0.000327	0.000326
South Asian	0.000290	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a regulator of microtubule physiology.

Recessive Scores

• pRec: 0.0965

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0939
• hipred: N
• hipred_score: 0.197
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nme9

Gene ontology

• Biological process: nucleoside diphosphate phosphorylation;GTP biosynthetic process;UTP biosynthetic process;CTP biosynthetic process;cell redox homeostasis
• Cellular component: cytoplasm;cytoskeleton
• Molecular function: nucleoside diphosphate kinase activity