NACA2

nascent polypeptide associated complex subunit alpha 2

Basic information

Region (hg38): 17:61590420-61591219

Previous symbols: [ "NACAL" ]

Links

ENSG00000253506 ∙ NCBI:342538 ∙ OMIM:609274 ∙ HGNC:23290 ∙ Uniprot:Q9H009 ∙ 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 NACA2 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NACA2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in NACA2

This is a list of pathogenic ClinVar variants found in the NACA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-61590568-C-A		not specified	Uncertain significance (Nov 08, 2022)
17-61590585-A-T		not specified	Uncertain significance (Jul 27, 2021)
17-61590606-C-T		not specified	Uncertain significance (Mar 07, 2023)
17-61590618-G-A		not specified	Uncertain significance (Feb 14, 2023)
17-61590624-G-A		not specified	Uncertain significance (Apr 07, 2023)
17-61590651-T-G		not specified	Uncertain significance (Jan 24, 2024)
17-61590722-A-C		not specified	Uncertain significance (Feb 13, 2024)
17-61590751-T-C		not specified	Uncertain significance (Apr 05, 2023)
17-61590796-G-T		not specified	Uncertain significance (Jan 30, 2024)
17-61590895-T-C		not specified	Uncertain significance (Mar 02, 2023)
17-61590900-A-G		not specified	Uncertain significance (Sep 06, 2022)
17-61591009-C-T		not specified	Uncertain significance (Feb 16, 2023)
17-61591029-G-T		not specified	Uncertain significance (May 18, 2022)
17-61591144-C-T		not specified	Uncertain significance (May 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NACA2	protein_coding	protein_coding	ENST00000521764	1	770

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0324	0.625	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00242	112	112	0.999	0.00000643	1382
Missense in Polyphen		28	24.027	1.1654		347
Synonymous	-1.57	61	47.3	1.29	0.00000322	442
Loss of Function	0.270	2	2.46	0.814	1.07e-7	29

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

• Function: FUNCTION: Prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER). Binds to nascent polypeptide chains as they emerge from the ribosome and blocks their interaction with the signal recognition particle (SRP), which normally targets nascent secretory peptides to the ER. Also reduces the inherent affinity of ribosomes for protein translocation sites in the ER membrane (M sites) (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.730
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.01

Haploinsufficiency Scores

• pHI: 0.712
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Gene ontology

• Biological process: protein transport
• Cellular component: nucleus;nascent polypeptide-associated complex