NECAB1

N-terminal EF-hand calcium binding protein 1, the group of EF-hand domain containing|N-terminal EF-hand calcium binding proteins

Basic information

Region (hg38): 8:90791741-90959393

Previous symbols: [ "EFCBP1" ]

Links

ENSG00000123119 ∙ NCBI:64168 ∙ ∙ HGNC:20983 ∙ Uniprot:Q8N987 ∙ 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 NECAB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECAB1 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				1		1
missense			10	1		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	10	2	0

Variants in NECAB1

This is a list of pathogenic ClinVar variants found in the NECAB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-90791918-C-T		not specified	Uncertain significance (Mar 21, 2022)
8-90824790-C-T			Likely benign (Apr 01, 2023)
8-90881042-C-G		not specified	Uncertain significance (Jun 11, 2021)
8-90881056-G-A		not specified	Uncertain significance (Dec 10, 2024)
8-90881074-G-C		not specified	Uncertain significance (Jun 10, 2022)
8-90881116-G-A		not specified	Uncertain significance (May 08, 2024)
8-90917618-C-T		not specified	Uncertain significance (May 03, 2023)
8-90925545-G-A		not specified	Likely benign (Mar 25, 2024)
8-90925587-T-A		not specified	Uncertain significance (Dec 20, 2023)
8-90928298-A-G		not specified	Uncertain significance (Dec 09, 2024)
8-90934337-A-C		not specified	Uncertain significance (Jun 23, 2023)
8-90934340-G-C		not specified	Uncertain significance (Jun 07, 2023)
8-90934355-T-G		not specified	Uncertain significance (May 27, 2022)
8-90940820-T-C		not specified	Uncertain significance (Feb 23, 2023)
8-90940879-T-C		not specified	Uncertain significance (Feb 16, 2023)
8-90949839-G-A		not specified	Uncertain significance (Nov 13, 2024)
8-90949846-G-A		not specified	Likely benign (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NECAB1	protein_coding	protein_coding	ENST00000417640	13	167859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0250	0.974	124615	0	12	124627	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	128	170	0.754	0.00000862	2313
Missense in Polyphen		27	49.716	0.54308		686
Synonymous	1.11	50	61.0	0.820	0.00000310	588
Loss of Function	3.04	7	22.6	0.309	0.00000115	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000582	0.0000582
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000539	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.0000366	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.500
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.384
• hipred: Y
• hipred_score: 0.738
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Necab1

Gene ontology

• Biological process: blastocyst hatching;biological_process;regulation of amyloid precursor protein biosynthetic process
• Cellular component: cellular_component;nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: molecular_function;calcium ion binding