NECAP2

NECAP endocytosis associated 2

Basic information

Region (hg38): 1:16440721-16460078

Links

ENSG00000157191 ∙ NCBI:55707 ∙ OMIM:611624 ∙ HGNC:25528 ∙ Uniprot:Q9NVZ3 ∙ 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 NECAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECAP2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	18	0	1

Variants in NECAP2

This is a list of pathogenic ClinVar variants found in the NECAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-16440774-G-C		not specified	Uncertain significance (Sep 17, 2021)
1-16440791-C-G			Benign (Dec 14, 2017)
1-16440811-A-G		not specified	Uncertain significance (Dec 21, 2022)
1-16440811-A-T		not specified	Uncertain significance (Jun 21, 2023)
1-16440829-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-16443672-C-T		not specified	Uncertain significance (May 21, 2024)
1-16443673-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-16447891-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-16447893-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-16447930-C-T		not specified	Uncertain significance (Apr 04, 2023)
1-16448066-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-16448089-G-A		not specified	Uncertain significance (Sep 02, 2024)
1-16448123-C-T		not specified	Uncertain significance (Nov 27, 2024)
1-16449174-G-T		Malignant tumor of prostate	Uncertain significance (-)
1-16451839-A-T		not specified	Uncertain significance (May 15, 2024)
1-16451875-G-C		not specified	Uncertain significance (Jul 30, 2024)
1-16451880-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-16451905-G-C		not specified	Uncertain significance (Mar 25, 2024)
1-16451911-T-C		not specified	Uncertain significance (Feb 26, 2024)
1-16451916-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-16451923-C-G		not specified	Uncertain significance (Nov 07, 2023)
1-16451932-A-C		not specified	Uncertain significance (Oct 05, 2023)
1-16458847-C-A		not specified	Uncertain significance (Dec 19, 2023)
1-16458884-G-C		not specified	Uncertain significance (Apr 28, 2022)
1-16458891-C-A		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NECAP2	protein_coding	protein_coding	ENST00000443980	7	19407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-9	0.133	125705	0	42	125747	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.270	150	160	0.940	0.00000884	1758
Missense in Polyphen		38	42.755	0.88879		499
Synonymous	-0.614	73	66.6	1.10	0.00000398	565
Loss of Function	0.253	14	15.1	0.930	8.97e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000352	0.000352
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000326	0.000326
South Asian	0.000264	0.000261
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endocytosis. {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.0975

Intolerance Scores

• loftool: 0.973
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.197
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Necap2

Gene ontology

• Biological process: endocytosis;protein transport
• Cellular component: plasma membrane;clathrin-coated pit;clathrin vesicle coat