NCLN

nicalin, the group of M28 metallopeptidases

Basic information

Region (hg38): 19:3185563-3209575

Links

ENSG00000125912 ∙ NCBI:56926 ∙ OMIM:609156 ∙ HGNC:26923 ∙ Uniprot:Q969V3 ∙ 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 NCLN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCLN 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			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	35	1	2

Variants in NCLN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-3186100-G-A		not specified	Uncertain significance (Jun 03, 2024)
19-3186112-G-A		not specified	Uncertain significance (Apr 05, 2023)
19-3186139-C-G		not specified	Uncertain significance (Nov 26, 2024)
19-3186179-G-T		not specified	Uncertain significance (Dec 14, 2022)
19-3192476-G-A		not specified	Uncertain significance (Feb 10, 2022)
19-3192529-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-3192548-G-A		not specified	Uncertain significance (Feb 05, 2024)
19-3192626-G-A		not specified	Uncertain significance (Jan 19, 2024)
19-3192637-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-3192647-A-G		not specified	Uncertain significance (Jul 27, 2021)
19-3192652-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-3192659-G-A			Likely benign (Jul 06, 2018)
19-3193315-C-T		not specified	Uncertain significance (May 30, 2024)
19-3193378-A-G		not specified	Uncertain significance (Feb 08, 2023)
19-3193404-C-T		Hirschsprung disease, susceptibility to, 1	Likely pathogenic (Sep 26, 2016)
19-3193413-G-A		not specified	Uncertain significance (Aug 23, 2021)
19-3196207-A-G		not specified	Uncertain significance (May 27, 2022)
19-3196209-G-A		not specified	Uncertain significance (Jun 27, 2022)
19-3196261-T-G		not specified	Uncertain significance (Mar 24, 2023)
19-3196286-C-T			Benign (Feb 16, 2018)
19-3198820-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-3198827-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-3198836-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-3201538-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-3201595-C-T		not specified	Uncertain significance (Sep 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCLN	protein_coding	protein_coding	ENST00000246117	15	24013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.755	0.245	125728	0	7	125735	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	255	341	0.748	0.0000239	3547
Missense in Polyphen		44	86.494	0.50871		870
Synonymous	-0.891	172	158	1.09	0.0000123	1138
Loss of Function	3.88	5	26.6	0.188	0.00000136	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000648	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000487	0.0000462
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000348	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May antagonize Nodal signaling and subsequent organization of axial structures during mesodermal patterning. {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.345
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.14

Haploinsufficiency Scores

• pHI: 0.673
• hipred: Y
• hipred_score: 0.685
• ghis: 0.549

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.837

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncln

Zebrafish Information Network

• Gene name: ncln
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: lacks all parts of type

Gene ontology

• Biological process: regulation of signal transduction;regulation of protein complex assembly;protein stabilization;regulation of protein complex stability
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane;protein-containing complex
• Molecular function: protein binding