NAA38

N-alpha-acetyltransferase 38, NatC auxiliary subunit, the group of LSm proteins|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): 17:7856685-7885238

Previous symbols: [ "LSMD1" ]

Links

ENSG00000183011 ∙ NCBI:84316 ∙ OMIM:617990 ∙ HGNC:28212 ∙ Uniprot:Q9BRA0 ∙ 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 NAA38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA38 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			16			16
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in NAA38

This is a list of pathogenic ClinVar variants found in the NAA38 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7856824-C-A		not specified	Uncertain significance (May 25, 2022)
17-7857066-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-7857186-C-G		not specified	Uncertain significance (Apr 06, 2022)
17-7857190-G-C		not specified	Uncertain significance (May 13, 2024)
17-7857198-C-T		not specified	Uncertain significance (Jan 03, 2024)
17-7857225-A-T		not specified	Uncertain significance (Jun 24, 2022)
17-7857256-C-T			Likely benign (Jan 01, 2018)
17-7857287-C-G		not specified	Uncertain significance (Mar 29, 2022)
17-7857289-C-A		not specified	Uncertain significance (Nov 28, 2023)
17-7857308-G-A		not specified	Uncertain significance (Sep 27, 2024)
17-7857311-G-A		not specified	Uncertain significance (Jun 04, 2024)
17-7857328-C-A		not specified	Uncertain significance (Sep 28, 2022)
17-7857328-C-G		not specified	Uncertain significance (Nov 08, 2024)
17-7857329-C-T		not specified	Uncertain significance (Sep 26, 2023)
17-7857335-C-T		not specified	Uncertain significance (Dec 12, 2023)
17-7857401-C-G		not specified	Uncertain significance (Feb 14, 2023)
17-7857408-C-G		not specified	Uncertain significance (Jan 24, 2024)
17-7858141-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-7858145-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-7858199-C-G		not specified	Uncertain significance (Dec 19, 2022)
17-7858225-C-T		not specified	Uncertain significance (Oct 06, 2021)
17-7858439-G-A		not specified	Uncertain significance (May 21, 2024)
17-7858450-A-G		not specified	Uncertain significance (Aug 04, 2023)
17-7858460-T-C		not specified	Uncertain significance (Oct 09, 2024)
17-7858475-G-A		not specified	Likely benign (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA38	protein_coding	protein_coding	ENST00000333775	2	28554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.71e-7	0.102	123449	15	2254	125718	0.00907

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.403	116	104	1.11	0.00000464	1069
Missense in Polyphen		19	26.792	0.70918		294
Synonymous	-1.65	61	46.7	1.31	0.00000210	398
Loss of Function	-0.802	8	5.90	1.36	2.56e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00976	0.00939
Ashkenazi Jewish	0.0160	0.0153
East Asian	0.000278	0.000272
Finnish	0.00229	0.00227
European (Non-Finnish)	0.0155	0.0145
Middle Eastern	0.000278	0.000272
South Asian	0.00296	0.00275
Other	0.0119	0.0113

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxillary component of the N-terminal acetyltransferase C (NatC) complex which catalyzes acetylation of N-terminal methionine residues. {ECO:0000269|PubMed:19398576}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0827

Intolerance Scores

• loftool: 0.665
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.730
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naa38

Gene ontology

• Biological process: negative regulation of apoptotic process
• Cellular component: nucleus;cytoplasm;polysome;NatC complex
• Molecular function: protein binding