NUTM2A

NUT family member 2A

Basic information

Region (hg38): 10:87225448-87236908

Previous symbols: [ "FAM22A" ]

Links

ENSG00000184923NCBI:728118HGNC:23438Uniprot:Q8IVF1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUTM2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUTM2A 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
68
clinvar
2
clinvar
70
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 68 2 0

Variants in NUTM2A

This is a list of pathogenic ClinVar variants found in the NUTM2A region.

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

Position Type Phenotype Significance ClinVar
10-87228286-G-A not specified Uncertain significance (Jun 24, 2022)2384973
10-87228287-T-C not specified Uncertain significance (Jan 31, 2025)3881965
10-87228308-C-T not specified Uncertain significance (Nov 07, 2022)2363000
10-87228331-C-T not specified Uncertain significance (May 20, 2024)3301646
10-87228352-G-A not specified Uncertain significance (Jul 13, 2021)2355805
10-87228388-G-T not specified Uncertain significance (May 23, 2023)2565206
10-87228389-C-T not specified Likely benign (Jul 20, 2021)2342955
10-87228478-G-T not specified Uncertain significance (Sep 08, 2024)3408947
10-87228482-C-G not specified Uncertain significance (Mar 19, 2024)3301642
10-87228501-G-A not specified Uncertain significance (Apr 17, 2023)2509502
10-87228511-G-T not specified Uncertain significance (Jul 06, 2022)2299887
10-87228529-G-A not specified Uncertain significance (Dec 05, 2022)2356295
10-87228559-G-A not specified Uncertain significance (Sep 20, 2024)3408942
10-87228560-C-G not specified Uncertain significance (Apr 17, 2024)3301645
10-87228565-C-A not specified Uncertain significance (Feb 17, 2022)3203357
10-87228568-G-A not specified Uncertain significance (Dec 02, 2024)2346515
10-87228586-G-A not specified Uncertain significance (Jan 01, 2025)3881964
10-87228599-G-C not specified Uncertain significance (May 31, 2023)2554642
10-87228613-C-T not specified Uncertain significance (Mar 26, 2024)3301641
10-87228628-G-C not specified Uncertain significance (May 27, 2022)2225921
10-87228734-C-T not specified Uncertain significance (Dec 10, 2024)3408944
10-87228757-G-T not specified Uncertain significance (Oct 22, 2021)2377090
10-87228764-A-G not specified Uncertain significance (Jan 10, 2023)3203358
10-87228779-C-G not specified Uncertain significance (Jul 05, 2022)2206681
10-87228789-A-C not specified Uncertain significance (Aug 17, 2022)2395446

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NUTM2Aprotein_codingprotein_codingENST00000381707 711461
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.36e-70.07321241820141241960.0000564
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6331071270.8420.000007235350
Missense in Polyphen3042.8690.69981708
Synonymous-1.517761.91.240.000004301852
Loss of Function-1.1385.211.542.24e-7245

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001190.000119
Ashkenazi Jewish0.000.00
East Asian0.0001180.000111
Finnish0.000.00
European (Non-Finnish)0.00003950.0000356
Middle Eastern0.0001180.000111
South Asian0.0001050.0000981
Other0.0001880.000165

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

pHI
0.0129
hipred
N
hipred_score
0.255
ghis
0.406

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nutm2
Phenotype