NCCRP1

NCCRP1, F-box associated domain containing

Basic information

Region (hg38): 19:39196964-39201884

Links

ENSG00000188505 ∙ NCBI:342897 ∙ OMIM:615901 ∙ HGNC:33739 ∙ Uniprot:Q6ZVX7 ∙ 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 NCCRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCCRP1 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in NCCRP1

This is a list of pathogenic ClinVar variants found in the NCCRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39196992-G-T		not specified	Uncertain significance (Jul 10, 2024)
19-39197013-G-C		not specified	Uncertain significance (Mar 18, 2024)
19-39197112-C-G		not specified	Uncertain significance (Sep 16, 2021)
19-39197140-C-T		not specified	Uncertain significance (Aug 15, 2024)
19-39197143-A-C		not specified	Uncertain significance (Jan 18, 2025)
19-39197167-C-T		not specified	Uncertain significance (Oct 06, 2024)
19-39197184-C-T		not specified	Uncertain significance (Sep 06, 2023)
19-39197218-C-A		not specified	Uncertain significance (Sep 12, 2023)
19-39197230-G-T		not specified	Uncertain significance (Nov 14, 2024)
19-39197253-A-G		not specified	Uncertain significance (May 03, 2023)
19-39197260-A-G		not specified	Uncertain significance (Jun 10, 2024)
19-39198069-G-T		not specified	Uncertain significance (Apr 23, 2024)
19-39198070-C-T		not specified	Uncertain significance (Oct 08, 2024)
19-39198098-G-A		not specified	Likely benign (Apr 07, 2023)
19-39198211-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-39198216-T-C		not specified	Uncertain significance (Sep 11, 2024)
19-39199170-C-G		not specified	Uncertain significance (Apr 22, 2024)
19-39199196-A-G		not specified	Uncertain significance (Jun 13, 2022)
19-39199211-G-A		not specified	Uncertain significance (Aug 26, 2024)
19-39199229-T-C		not specified	Uncertain significance (Jan 18, 2025)
19-39199237-G-A		not specified	Uncertain significance (Apr 23, 2024)
19-39199240-C-A		not specified	Uncertain significance (Aug 31, 2022)
19-39199259-T-C		not specified	Uncertain significance (Sep 12, 2023)
19-39199262-A-C		not specified	Uncertain significance (Aug 02, 2021)
19-39200350-G-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCCRP1	protein_coding	protein_coding	ENST00000339852	6	4924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.64e-9	0.153	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.317	152	163	0.930	0.0000105	1706
Missense in Polyphen		71	72.263	0.98252		738
Synonymous	-0.505	75	69.6	1.08	0.00000430	610
Loss of Function	0.229	13	13.9	0.934	7.29e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00147
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell proliferation. {ECO:0000269|PubMed:22087255}.

Recessive Scores

• pRec: 0.136

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.311
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nccrp1

Gene ontology

• Biological process: positive regulation of cell population proliferation
• Cellular component: cytoplasm;extracellular exosome