NCR3LG1

natural killer cell cytotoxicity receptor 3 ligand 1, the group of Receptor ligands|B7 family|C1-set domain containing

Basic information

Region (hg38): 11:17351800-17377341

Links

ENSG00000188211 ∙ NCBI:374383 ∙ OMIM:613714 ∙ HGNC:42400 ∙ Uniprot:Q68D85 ∙ 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 NCR3LG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCR3LG1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in NCR3LG1

This is a list of pathogenic ClinVar variants found in the NCR3LG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-17351974-C-A		not specified	Uncertain significance (May 24, 2023)
11-17352034-C-T		not specified	Uncertain significance (Nov 08, 2022)
11-17356687-A-G		not specified	Uncertain significance (Aug 04, 2021)
11-17356708-A-G		not specified	Likely benign (May 20, 2024)
11-17356728-A-G		not specified	Likely benign (Feb 17, 2022)
11-17356761-A-G		not specified	Uncertain significance (May 03, 2023)
11-17356798-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-17356820-A-C		not specified	Uncertain significance (Jun 24, 2022)
11-17356849-G-A		not specified	Uncertain significance (Jun 27, 2023)
11-17356858-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-17356869-C-A		not specified	Uncertain significance (May 03, 2023)
11-17356902-C-T		not specified	Uncertain significance (Apr 24, 2024)
11-17356903-G-T		not specified	Uncertain significance (Jul 17, 2023)
11-17367104-A-G		not specified	Uncertain significance (Dec 21, 2022)
11-17367116-T-C		not specified	Uncertain significance (Dec 09, 2023)
11-17367161-G-A		not specified	Uncertain significance (Sep 26, 2023)
11-17367168-T-A		not specified	Uncertain significance (Apr 04, 2023)
11-17368911-T-A		not specified	Uncertain significance (Jul 21, 2021)
11-17368941-A-T		not specified	Uncertain significance (Sep 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCR3LG1	protein_coding	protein_coding	ENST00000338965	5	25616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000886	0.797	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	157	229	0.686	0.0000111	2926
Missense in Polyphen		24	47.956	0.50046		643
Synonymous	1.58	74	93.4	0.792	0.00000482	922
Loss of Function	1.18	8	12.5	0.641	6.98e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Triggers NCR3-dependent natural killer cell activation. {ECO:0000269|PubMed:19528259}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Haploinsufficiency Scores

• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: structural molecule activity;protein binding