NABP2

nucleic acid binding protein 2

Basic information

Region (hg38): 12:56222014-56229854

Previous symbols: [ "OBFC2B" ]

Links

ENSG00000139579 ∙ NCBI:79035 ∙ OMIM:612104 ∙ HGNC:28412 ∙ Uniprot:Q9BQ15 ∙ 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 NABP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NABP2 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in NABP2

This is a list of pathogenic ClinVar variants found in the NABP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56224929-G-A		not specified	Uncertain significance (Feb 17, 2022)
12-56225396-G-A		not specified	Uncertain significance (Aug 18, 2021)
12-56225635-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-56226410-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-56229061-G-A		not specified	Uncertain significance (Mar 17, 2023)
12-56229064-G-A		not specified	Uncertain significance (Mar 01, 2023)
12-56229092-C-T		not specified	Uncertain significance (Oct 13, 2023)
12-56229094-C-T		not specified	Uncertain significance (May 10, 2024)
12-56229158-C-T		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NABP2	protein_coding	protein_coding	ENST00000380198	6	7840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0274	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	74	125	0.591	0.00000707	1358
Missense in Polyphen		22	59.55	0.36943		630
Synonymous	-0.120	49	47.9	1.02	0.00000293	433
Loss of Function	3.09	0	11.1	0.00	7.14e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the SOSS complex, a multiprotein complex that functions downstream of the MRN complex to promote DNA repair and G2/M checkpoint. In the SOSS complex, acts as a sensor of single-stranded DNA that binds to single-stranded DNA, in particular to polypyrimidines. The SOSS complex associates with DNA lesions and influences diverse endpoints in the cellular DNA damage response including cell-cycle checkpoint activation, recombinational repair and maintenance of genomic stability. Required for efficient homologous recombination-dependent repair of double-strand breaks (DSBs) and ATM-dependent signaling pathways. {ECO:0000269|PubMed:18449195, ECO:0000269|PubMed:19605351, ECO:0000269|PubMed:19683501}.
• Pathway: Mesodermal Commitment Pathway;Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.295
• hipred: Y
• hipred_score: 0.775
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nabp2
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; neoplasm; hematopoietic system phenotype; reproductive system 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); respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: double-strand break repair via homologous recombination;DNA repair;cellular response to DNA damage stimulus;mitotic cell cycle checkpoint;response to ionizing radiation;snRNA transcription by RNA polymerase II;regulation of telomerase activity;establishment of protein localization to telomere;positive regulation of telomere capping
• Cellular component: nuclear chromosome, telomeric region;nucleus;nucleoplasm;cytosol;SOSS complex
• Molecular function: single-stranded DNA binding;protein binding;C-rich strand telomeric DNA binding;DNA polymerase binding;G-rich strand telomeric DNA binding