NUTM2A

Gene

NUT family member 2A

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

FAM22A

MANE transcript

NM_001099338.2

Inheritance

—

ClinVar variants

U:141B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.54

Max pathogenic AF

—

Genomic locus

chr10:87,225,448-87,236,908

External References & Databases

Ensembl (ENSG00000184923)

Transcript & Mutation Effects

hg38 • Region Span ~11.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUTM2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 143

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099338.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			141 clinvar	2 clinvar		143
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	141	3	0	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099338.2	RefSeq	NP_001092808.1	7	MANE Select
ENST00000381707.6	Ensembl	ENSP00000371126.1	7	MANE Select
ENST00000381689.4	Ensembl	ENSP00000371107.3	7	Standard
ENST00000381689.5	Ensembl	ENSP00000371107.3	7	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381707
Coding exons: 7
Length: 11461
Individuals with no LoFs: 124182
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124196
p: 0.0000564

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.633	107	127	0.842	0.00000723	5350
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000040	0.000036	rare
South Asian	0.00010	0.000098	rare
Other	0.00019	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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