NABP1

nucleic acid binding protein 1

Basic information

Region (hg38): 2:191678068-191741097

Previous symbols: [ "OBFC2A", "NABP1-OT1" ]

Links

ENSG00000173559 ∙ NCBI:64859 ∙ OMIM:612103 ∙ HGNC:26232 ∙ Uniprot:Q96AH0 ∙ 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 NABP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NABP1 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	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	17	1	0

Variants in NABP1

This is a list of pathogenic ClinVar variants found in the NABP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-191678628-A-G		not specified	Uncertain significance (Dec 21, 2023)
2-191678651-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-191678655-T-C		not specified	Uncertain significance (Dec 17, 2023)
2-191678673-A-G		not specified	Uncertain significance (Feb 27, 2023)
2-191678684-G-A		not specified	Uncertain significance (Sep 01, 2024)
2-191678992-C-T		not specified	Uncertain significance (Jun 05, 2023)
2-191678993-G-A		not specified	Uncertain significance (Oct 03, 2023)
2-191679013-G-A		not specified	Uncertain significance (Aug 28, 2023)
2-191679086-G-C		not specified	Uncertain significance (Mar 01, 2025)
2-191679094-A-T		not specified	Uncertain significance (Jan 07, 2025)
2-191681996-G-T		not specified	Uncertain significance (Jan 31, 2024)
2-191683739-G-A		not specified	Uncertain significance (Nov 30, 2021)
2-191683802-G-C		not specified	Uncertain significance (May 08, 2023)
2-191685620-C-G		not specified	Uncertain significance (Nov 13, 2024)
2-191685623-A-G		not specified	Uncertain significance (May 27, 2022)
2-191685637-C-G		not specified	Uncertain significance (Mar 22, 2023)
2-191685667-C-T		not specified	Uncertain significance (May 24, 2024)
2-191685697-A-G		not specified	Likely benign (Nov 21, 2023)
2-191685706-A-G		not specified	Uncertain significance (Dec 20, 2023)
2-191685745-C-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NABP1	protein_coding	protein_coding	ENST00000425611	6	18592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000328	0.591	125722	1	25	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0314	110	111	0.992	0.00000540	1333
Missense in Polyphen		26	30.711	0.8466		390
Synonymous	1.67	25	38.1	0.655	0.00000177	385
Loss of Function	0.746	8	10.6	0.753	5.14e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000903	0.0000903
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000232	0.000163
Other	0.000495	0.000489

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:19605351, ECO:0000269|PubMed:19683501}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0857

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.194
• hipred: Y
• hipred_score: 0.706
• ghis: 0.555

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nabp1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland 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
• Cellular component: nuclear chromosome, telomeric region;nucleus;nucleoplasm;cytosol;SOSS complex
• Molecular function: single-stranded DNA binding;RNA binding;protein binding