NAB1

NGFI-A binding protein 1

Basic information

Region (hg38): 2:190646745-190692766

Links

ENSG00000138386 ∙ NCBI:4664 ∙ OMIM:600800 ∙ HGNC:7626 ∙ Uniprot:Q13506 ∙ 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 NAB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAB1 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in NAB1

This is a list of pathogenic ClinVar variants found in the NAB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-190659486-C-T		not specified	Uncertain significance (Apr 01, 2024)
2-190659492-T-C		not specified	Uncertain significance (Aug 04, 2023)
2-190659571-C-T		not specified	Uncertain significance (Mar 20, 2023)
2-190659589-G-C		not specified	Uncertain significance (Feb 10, 2023)
2-190659640-T-C		not specified	Uncertain significance (Jan 31, 2022)
2-190659720-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-190659722-G-A		not specified	Likely benign (May 12, 2024)
2-190659787-A-G		not specified	Uncertain significance (Nov 17, 2022)
2-190659790-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-190659798-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-190659818-C-A		not specified	Uncertain significance (Aug 02, 2021)
2-190659879-A-G		not specified	Uncertain significance (Oct 05, 2023)
2-190659886-A-C		not specified	Uncertain significance (Jun 17, 2024)
2-190670348-C-T		not specified	Uncertain significance (May 23, 2024)
2-190670359-G-A		not specified	Uncertain significance (Jul 15, 2021)
2-190670380-A-T		not specified	Uncertain significance (Jun 14, 2023)
2-190673108-T-C		not specified	Uncertain significance (Jun 29, 2023)
2-190673147-G-A		not specified	Uncertain significance (Feb 13, 2024)
2-190683774-C-G		not specified	Uncertain significance (Oct 03, 2022)
2-190683795-A-G		not specified	Uncertain significance (Sep 01, 2021)
2-190685522-A-G		not specified	Uncertain significance (Jan 09, 2024)
2-190685538-A-T		not specified	Uncertain significance (Jun 02, 2024)
2-190685545-C-G		not specified	Uncertain significance (Oct 20, 2021)
2-190685551-G-A		not specified	Uncertain significance (Jan 18, 2023)
2-190685557-A-G		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAB1	protein_coding	protein_coding	ENST00000337386	7	46021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0219	0.977	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	194	255	0.762	0.0000125	3173
Missense in Polyphen		63	99.155	0.63537		1283
Synonymous	0.453	95	101	0.943	0.00000542	938
Loss of Function	3.00	7	22.3	0.314	0.00000115	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000194	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor for zinc finger transcription factors EGR1 and EGR2. {ECO:0000250}.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.106
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.361
• hipred: Y
• hipred_score: 0.783
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nab1
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: endochondral ossification;regulation of transcription, DNA-templated;Schwann cell differentiation;myelination;regulation of epidermis development;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: transcription factor binding