NACA

nascent polypeptide associated complex subunit alpha

Basic information

Region (hg38): 12:56712305-56731628

Links

ENSG00000196531 ∙ NCBI:4666 ∙ OMIM:601234 ∙ HGNC:7629 ∙ Uniprot:E9PAV3, Q13765 ∙ 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 NACA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NACA 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				8	1	9
missense			44	3	3	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	11	4

Variants in NACA

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

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

Position	Type	Phenotype	Significance	ClinVar
12-56713102-G-A		not specified	Uncertain significance (Jun 18, 2024)
12-56713602-T-C		not specified	Uncertain significance (Jan 16, 2024)
12-56713628-C-T		not specified	Uncertain significance (May 09, 2022)
12-56715898-T-C		not specified	Uncertain significance (Oct 12, 2021)
12-56715948-T-C		not specified	Uncertain significance (Jun 04, 2024)
12-56715958-C-T		not specified	Uncertain significance (Oct 27, 2022)
12-56715960-G-A		not specified	Uncertain significance (Oct 08, 2024)
12-56715973-C-T		not specified	Uncertain significance (May 16, 2023)
12-56715993-G-A		not specified	Uncertain significance (Sep 06, 2022)
12-56715997-G-A		not specified	Uncertain significance (Aug 07, 2024)
12-56716003-G-C		not specified	Uncertain significance (Jan 10, 2022)
12-56716046-G-C			Likely benign (Apr 01, 2022)
12-56716126-G-A		not specified	Uncertain significance (May 23, 2023)
12-56716182-G-C		not specified	Uncertain significance (Dec 27, 2022)
12-56716183-G-T		not specified	Uncertain significance (Sep 02, 2024)
12-56716190-C-A		not specified	Uncertain significance (Apr 09, 2024)
12-56716195-C-T		not specified	Uncertain significance (Nov 30, 2022)
12-56716216-G-A			Benign (Jul 16, 2018)
12-56717744-C-T			Likely benign (Jun 01, 2022)
12-56717921-G-A			Likely benign (Nov 01, 2022)
12-56718080-T-A			Likely benign (Nov 01, 2022)
12-56718128-G-A			Likely benign (Jul 01, 2024)
12-56718260-T-G			Likely benign (Jan 01, 2024)
12-56718533-A-G			Likely benign (May 01, 2024)
12-56718638-T-C			Likely benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NACA	protein_coding	protein_coding	ENST00000550952	10	19201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000473	0.999	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.896	424	479	0.885	0.0000227	5803
Missense in Polyphen		17	24.181	0.70303		359
Synonymous	-0.262	190	185	1.02	0.00000917	2156
Loss of Function	2.78	12	27.8	0.431	0.00000126	365

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cardiac- and muscle-specific transcription factor. May act to regulate the expression of genes involved in the development of myotubes. Plays a critical role in ventricular cardiomyocyte expansion and regulates postnatal skeletal muscle growth and regeneration. Involved in the organized assembly of thick and thin filaments of myofibril sarcomeres (By similarity). {ECO:0000250|UniProtKB:P70670}.
• Pathway: Integrin-linked kinase signaling (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.531
• rvis_EVS: 1.65
• rvis_percentile_EVS: 96.18

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.301
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naca
• Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: naca
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Cellular component: nucleus;nascent polypeptide-associated complex
• Molecular function: DNA binding