NUTM2B

NUT family member 2B

Basic information

Region (hg38): 10:79703226-79714681

Previous symbols: [ "FAM22B" ]

Links

ENSG00000188199 ∙ NCBI:729262 ∙ ∙ HGNC:23445 ∙ Uniprot:A6NNL0 ∙ 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 NUTM2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUTM2B 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				3		3
missense				3		3
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	6	2

Variants in NUTM2B

This is a list of pathogenic ClinVar variants found in the NUTM2B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-79706577-T-C			Likely benign (Nov 01, 2023)
10-79706584-A-G			Likely benign (Aug 01, 2023)
10-79710644-C-T			Likely benign (Dec 31, 2019)
10-79710716-C-T			Likely benign (Mar 01, 2023)
10-79711875-T-C		not specified	Benign/Likely benign (-)
10-79711884-G-A			Likely benign (Sep 01, 2022)
10-79711899-G-A			Likely benign (Nov 01, 2023)
10-79712337-CTGAAAAGACA-C		Oculopharyngeal myopathy with leukoencephalopathy 1	Benign (Jan 02, 2020)
10-79712349-CCT-C		Oculopharyngeal myopathy with leukoencephalopathy 1	Benign (Jan 02, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUTM2B	protein_coding	protein_coding	ENST00000429828	7	11455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0205	0.762	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.888	133	165	0.806	0.00000904	5399
Missense in Polyphen		27	33.18	0.81374		1589
Synonymous	0.199	66	68.1	0.969	0.00000388	1860
Loss of Function	0.864	3	5.11	0.588	2.33e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.431
• ghis: 0.470

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