NUTM2A

NUT family member 2A

Basic information

Region (hg38): 10:87225448-87236908

Previous symbols: [ "FAM22A" ]

Links

ENSG00000184923 ∙ NCBI:728118 ∙ ∙ HGNC:23438 ∙ Uniprot:Q8IVF1 ∙ 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 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	2		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)
10-87228287-T-C		not specified	Uncertain significance (Jan 31, 2025)
10-87228308-C-T		not specified	Uncertain significance (Nov 07, 2022)
10-87228331-C-T		not specified	Uncertain significance (May 20, 2024)
10-87228352-G-A		not specified	Uncertain significance (Jul 13, 2021)
10-87228388-G-T		not specified	Uncertain significance (May 23, 2023)
10-87228389-C-T		not specified	Likely benign (Jul 20, 2021)
10-87228478-G-T		not specified	Uncertain significance (Sep 08, 2024)
10-87228482-C-G		not specified	Uncertain significance (Mar 19, 2024)
10-87228501-G-A		not specified	Uncertain significance (Apr 17, 2023)
10-87228511-G-T		not specified	Uncertain significance (Jul 06, 2022)
10-87228529-G-A		not specified	Uncertain significance (Dec 05, 2022)
10-87228559-G-A		not specified	Uncertain significance (Sep 20, 2024)
10-87228560-C-G		not specified	Uncertain significance (Apr 17, 2024)
10-87228565-C-A		not specified	Uncertain significance (Feb 17, 2022)
10-87228568-G-A		not specified	Uncertain significance (Dec 02, 2024)
10-87228586-G-A		not specified	Uncertain significance (Jan 01, 2025)
10-87228599-G-C		not specified	Uncertain significance (May 31, 2023)
10-87228613-C-T		not specified	Uncertain significance (Mar 26, 2024)
10-87228628-G-C		not specified	Uncertain significance (May 27, 2022)
10-87228734-C-T		not specified	Uncertain significance (Dec 10, 2024)
10-87228757-G-T		not specified	Uncertain significance (Oct 22, 2021)
10-87228764-A-G		not specified	Uncertain significance (Jan 10, 2023)
10-87228779-C-G		not specified	Uncertain significance (Jul 05, 2022)
10-87228789-A-C		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUTM2A	protein_coding	protein_coding	ENST00000381707	7	11461

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.36e-7	0.0732	124182	0	14	124196	0.0000564

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.633	107	127	0.842	0.00000723	5350
Missense in Polyphen		30	42.869	0.6998		1708
Synonymous	-1.51	77	61.9	1.24	0.00000430	1852
Loss of Function	-1.13	8	5.21	1.54	2.24e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000118	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000395	0.0000356
Middle Eastern	0.000118	0.000111
South Asian	0.000105	0.0000981
Other	0.000188	0.000165

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0129
• hipred: N
• hipred_score: 0.255
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nutm2