NECAB3

N-terminal EF-hand calcium binding protein 3, the group of N-terminal EF-hand calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 20:33657086-33674463

Previous symbols: [ "SYTIP2", "APBA2BP" ]

Links

ENSG00000125967 ∙ NCBI:63941 ∙ OMIM:612478 ∙ HGNC:15851 ∙ Uniprot:Q96P71 ∙ 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 NECAB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECAB3 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			16	3		19
Total	0	0	35	5	0

Variants in NECAB3

This is a list of pathogenic ClinVar variants found in the NECAB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33657974-G-A		not specified	Uncertain significance (Dec 11, 2023)
20-33657978-G-A		not specified	Uncertain significance (Jul 06, 2022)
20-33658765-G-A		not specified	Likely benign (Dec 20, 2021)
20-33659581-C-G		not specified	Uncertain significance (Jan 03, 2024)
20-33659603-G-A		not specified	Likely benign (May 24, 2023)
20-33659661-C-T		not specified	Uncertain significance (Apr 25, 2023)
20-33659673-T-C		not specified	Uncertain significance (Feb 21, 2024)
20-33659703-G-A		not specified	Uncertain significance (Mar 16, 2022)
20-33659903-G-A		not specified	Uncertain significance (Feb 27, 2024)
20-33659907-C-A		not specified	Uncertain significance (Aug 23, 2021)
20-33659939-C-T		not specified	Uncertain significance (Jul 25, 2023)
20-33659942-G-C		not specified	Uncertain significance (Jun 18, 2021)
20-33659945-G-A		not specified	Uncertain significance (Dec 05, 2022)
20-33659954-G-A		not specified	Uncertain significance (Dec 28, 2023)
20-33659963-C-T		not specified	Uncertain significance (Oct 18, 2021)
20-33659970-C-G		not specified	Uncertain significance (Apr 30, 2024)
20-33660260-G-A		not specified	Uncertain significance (Oct 13, 2023)
20-33660337-G-A		not specified	Uncertain significance (May 26, 2024)
20-33660358-G-A		not specified	Uncertain significance (Feb 21, 2024)
20-33662436-T-C		not specified	Likely benign (Aug 09, 2021)
20-33663757-T-G		not specified	Uncertain significance (Sep 15, 2021)
20-33663763-C-G		not specified	Uncertain significance (Jul 13, 2021)
20-33663844-C-G		not specified	Uncertain significance (Oct 29, 2021)
20-33667502-C-G		not specified	Uncertain significance (Feb 06, 2024)
20-33667542-C-G		not specified	Likely benign (Mar 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NECAB3	protein_coding	protein_coding	ENST00000246190	12	17377

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000275	0.985	124778	0	18	124796	0.0000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.964	179	219	0.817	0.0000139	2510
Missense in Polyphen		59	79.019	0.74665		949
Synonymous	0.357	86	90.3	0.952	0.00000567	791
Loss of Function	2.18	11	22.0	0.500	0.00000103	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000228	0.000211
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000646	0.0000618
Middle Eastern	0.000223	0.000223
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the interaction of APBA2 with amyloid-beta precursor protein (APP), and hence allows formation of amyloid- beta. May enhance the activity of HIF1A and thus promote glycolysis under normoxic conditions; the function requires its ABM domain and may implicate the stabilization of the interaction between HIF1AN and APBA3. {ECO:0000269|PubMed:10833507, ECO:0000269|PubMed:26948053}.

Recessive Scores

• pRec: 0.0899

Haploinsufficiency Scores

• pHI: 0.206
• hipred: Y
• hipred_score: 0.682
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Necab3

Gene ontology

• Biological process: protein secretion;protein metabolic process;regulation of amyloid precursor protein biosynthetic process
• Cellular component: Golgi cis cisterna;nucleus;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus
• Molecular function: calcium ion binding;protein binding