NUTM2F

NUT family member 2F

Basic information

Region (hg38): 9:94318198-94328644

Previous symbols: [ "FAM22F" ]

Links

ENSG00000130950 ∙ NCBI:54754 ∙ ∙ HGNC:23450 ∙ Uniprot:A1L443 ∙ 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 NUTM2F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUTM2F 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			71	7		78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	71	8	0

Variants in NUTM2F

This is a list of pathogenic ClinVar variants found in the NUTM2F region.

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

Position	Type	Phenotype	Significance	ClinVar
9-94318479-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-94318482-G-A		not specified	Uncertain significance (Jun 13, 2024)
9-94318601-G-A		not specified	Uncertain significance (Mar 05, 2025)
9-94318616-G-A		not specified	Uncertain significance (Mar 08, 2024)
9-94318617-G-A		not specified	Uncertain significance (Feb 08, 2025)
9-94318676-C-A		not specified	Uncertain significance (Jan 02, 2024)
9-94318731-C-T		not specified	Uncertain significance (Oct 29, 2021)
9-94318765-G-A			Likely benign (Feb 01, 2024)
9-94318787-C-T		not specified	Uncertain significance (Mar 25, 2024)
9-94318809-C-T		not specified	Uncertain significance (Jan 24, 2024)
9-94318827-G-A		not specified	Uncertain significance (Jan 26, 2025)
9-94318835-G-A		not specified	Uncertain significance (Jan 10, 2022)
9-94318896-G-T		not specified	Uncertain significance (Aug 01, 2024)
9-94318955-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-94318965-G-A		not specified	Uncertain significance (Dec 14, 2023)
9-94319031-T-C		not specified	Uncertain significance (Apr 19, 2023)
9-94319040-G-A		not specified	Likely benign (Sep 09, 2024)
9-94319042-A-G		not specified	Uncertain significance (Jan 09, 2024)
9-94319069-G-A		not specified	Uncertain significance (Jun 06, 2023)
9-94319075-G-A		not specified	Uncertain significance (Dec 05, 2022)
9-94319097-C-T		not specified	Likely benign (Mar 20, 2024)
9-94319192-C-G		not specified	Uncertain significance (Jan 23, 2024)
9-94319234-A-G		not specified	Uncertain significance (Jun 11, 2021)
9-94319673-C-A		not specified	Uncertain significance (Jul 09, 2021)
9-94319680-T-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUTM2F	protein_coding	protein_coding	ENST00000253262	7	13322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-9	0.359	124765	1	73	124839	0.000296

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.408	406	384	1.06	0.0000220	4729
Missense in Polyphen		113	108.93	1.0373		1579
Synonymous	0.521	159	168	0.949	0.0000105	1656
Loss of Function	0.831	15	18.9	0.794	0.00000104	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000519	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.000891	0.000884
Finnish	0.00	0.00
European (Non-Finnish)	0.000322	0.000309
Middle Eastern	0.000891	0.000884
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0218
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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