NAA20

N-alpha-acetyltransferase 20, NatB catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): 20:20017309-20033655

Previous symbols: [ "NAT5" ]

Links

ENSG00000173418 ∙ NCBI:51126 ∙ OMIM:610833 ∙ HGNC:15908 ∙ Uniprot:P61599 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, autosomal recessive 73 (Limited), mode of inheritance: AR
• intellectual developmental disorder, autosomal recessive 73 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 73	AR	Cardiovascular	Among other findings, the condition can include congenital cardiac anomalies, and awareness may allow early intervention and management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	34230638

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAA20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA20 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		1	7			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	7	0	0

Variants in NAA20

This is a list of pathogenic ClinVar variants found in the NAA20 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-20017412-G-A		not specified	Uncertain significance (Feb 23, 2023)
20-20025758-A-G		Intellectual developmental disorder, autosomal recessive 73	Likely pathogenic (Mar 17, 2024)
20-20026805-C-T		not specified	Uncertain significance (Jan 22, 2024)
20-20026853-C-T		Intellectual developmental disorder, autosomal recessive 73	Pathogenic (Jan 27, 2022)
20-20026871-T-C		not specified	Uncertain significance (Feb 03, 2022)
20-20026904-A-T		not specified	Uncertain significance (Nov 09, 2021)
20-20032542-G-A		not specified	Uncertain significance (Dec 01, 2022)
20-20032605-A-G		not specified	Uncertain significance (Sep 22, 2023)
20-20033125-G-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA20	protein_coding	protein_coding	ENST00000334982	6	16540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00620	0.916	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	65	102	0.635	0.00000523	1160
Missense in Polyphen		10	24.966	0.40055		287
Synonymous	-0.552	42	37.7	1.11	0.00000225	334
Loss of Function	1.52	5	10.2	0.488	4.97e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000350	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000693	0.000693
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the NatB complex which catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Asp, Met-Glu, Met-Asn and Met-Gln. Proteins with cell cycle functions are overrepresented in the pool of NatB substrates. Required for maintaining the structure and function of actomyosin fibers and for proper cellular migration. {ECO:0000269|PubMed:18570629}.
• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.0948

Intolerance Scores

• loftool: 0.798
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.351
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.730

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naa20

Gene ontology

• Biological process: N-terminal peptidyl-methionine acetylation
• Cellular component: nucleus;cytoplasm;cytosol;NatB complex
• Molecular function: peptide alpha-N-acetyltransferase activity