NME7

NME/NM23 family member 7, the group of NME/NM23 family|Cilia and flagella associated

Basic information

Region (hg38): 1:169132530-169367948

Links

ENSG00000143156 ∙ NCBI:29922 ∙ OMIM:613465 ∙ HGNC:20461 ∙ Uniprot:Q9Y5B8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• situs inversus (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NME7 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NME7 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in NME7

This is a list of pathogenic ClinVar variants found in the NME7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-169132806-G-GAAGT		NME7-related disorder	Likely benign (Aug 30, 2023)
1-169169493-T-C		not specified	Uncertain significance (Apr 04, 2023)
1-169169545-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-169230725-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-169230774-T-C		not specified	Uncertain significance (Mar 22, 2023)
1-169230792-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-169235165-T-C		not specified	Uncertain significance (Aug 02, 2023)
1-169237670-G-C		not specified	Uncertain significance (Jan 30, 2024)
1-169287356-G-A		not specified	Uncertain significance (Nov 10, 2022)
1-169287365-G-C		not specified	Uncertain significance (Mar 05, 2024)
1-169287377-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-169298590-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-169298605-C-A		not specified	Uncertain significance (Sep 29, 2023)
1-169298666-T-C		not specified	Uncertain significance (Jun 30, 2023)
1-169298668-G-T		not specified	Uncertain significance (Sep 07, 2022)
1-169298756-T-C		not specified	Uncertain significance (Mar 29, 2022)
1-169303169-T-C		not specified	Uncertain significance (Oct 10, 2023)
1-169309980-T-C		not specified	Uncertain significance (Dec 08, 2023)
1-169310040-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-169323151-A-T		not specified	Uncertain significance (Nov 21, 2022)
1-169323203-G-C		not specified	Uncertain significance (Jan 06, 2023)
1-169323249-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-169324437-G-A		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NME7	protein_coding	protein_coding	ENST00000367811	12	235437

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000405	0.955	125698	0	48	125746	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.505	184	204	0.901	0.0000107	2472
Missense in Polyphen		38	44.693	0.85024		535
Synonymous	0.462	62	66.8	0.928	0.00000328	698
Loss of Function	1.88	12	21.4	0.561	0.00000118	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000538	0.000533
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.000163	0.000163
South Asian	0.000171	0.000163
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;UTP and CTP <i>de novo</i> biosynthesis;Metabolism of nucleotides;Folate metabolism;purine deoxyribonucleosides salvage;Interconversion of nucleotide di- and triphosphates;Metabolism;superpathway of pyrimidine ribonucleotides <i>de novo</i> biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;Purine nucleotides nucleosides metabolism;CMP phosphorylation;superpathway of purine nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP;guanosine deoxyribonucleotides <i>de novo</i> biosynthesis;guanosine nucleotides <i>de novo</i> biosynthesis;adenosine deoxyribonucleotides <i>de novo</i> biosynthesis;guanosine ribonucleotides <i>de novo</i> biosynthesis;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.790
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.849
• hipred: Y
• hipred_score: 0.659
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nme7
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; respiratory system 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); craniofacial phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: nucleoside diphosphate phosphorylation;GTP biosynthetic process;UTP biosynthetic process;CTP biosynthetic process
• Cellular component: centrosome;cytosol
• Molecular function: nucleoside diphosphate kinase activity;protein binding;ATP binding;metal ion binding