NHLRC3

NHL repeat containing 3

Basic information

Region (hg38): 13:39038306-39050109

Links

ENSG00000188811 ∙ NCBI:387921 ∙ ∙ HGNC:33751 ∙ Uniprot:Q5JS37 ∙ 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 NHLRC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NHLRC3 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			27			27
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	28	0	0

Variants in NHLRC3

This is a list of pathogenic ClinVar variants found in the NHLRC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-39038644-C-G		not specified	Uncertain significance (Feb 12, 2024)
13-39038652-T-G		not specified	Uncertain significance (Oct 16, 2023)
13-39038665-C-T		not specified	Uncertain significance (Oct 07, 2024)
13-39038682-C-T		not specified	Uncertain significance (Dec 19, 2023)
13-39039157-G-A		not specified	Uncertain significance (Jan 08, 2024)
13-39039187-T-C		not specified	Uncertain significance (May 06, 2024)
13-39039202-G-T		not specified	Uncertain significance (Mar 29, 2023)
13-39039218-C-G		not specified	Uncertain significance (Dec 13, 2024)
13-39039232-G-A		not specified	Uncertain significance (Sep 16, 2021)
13-39039263-T-C		not specified	Uncertain significance (Sep 16, 2021)
13-39039272-T-C		not specified	Uncertain significance (Dec 16, 2023)
13-39039646-C-T		not specified	Uncertain significance (Apr 17, 2023)
13-39039648-C-T		not specified	Uncertain significance (Aug 05, 2024)
13-39039649-A-G		not specified	Uncertain significance (Dec 31, 2024)
13-39039685-C-A		not specified	Uncertain significance (Nov 18, 2022)
13-39039702-G-A		not specified	Uncertain significance (May 23, 2023)
13-39042126-A-G		not specified	Uncertain significance (May 15, 2024)
13-39042165-G-C		not specified	Uncertain significance (Jul 27, 2021)
13-39042219-C-T		not specified	Uncertain significance (Mar 08, 2025)
13-39042222-A-G		not specified	Uncertain significance (Mar 07, 2024)
13-39042228-A-G		not specified	Uncertain significance (Oct 10, 2023)
13-39042267-A-T		not specified	Uncertain significance (Jan 19, 2025)
13-39042294-A-G		not specified	Uncertain significance (Feb 28, 2023)
13-39044154-C-G		not specified	Uncertain significance (Dec 11, 2024)
13-39047045-G-T		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NHLRC3	protein_coding	protein_coding	ENST00000379600	7	11804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000185	0.895	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	171	182	0.939	0.00000854	2246
Missense in Polyphen		55	63.695	0.86349		782
Synonymous	0.546	62	67.7	0.916	0.00000324	691
Loss of Function	1.54	10	16.8	0.595	8.97e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000396	0.000396
Middle Eastern	0.000164	0.000163
South Asian	0.00108	0.00108
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.326
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.0499
• hipred: N
• hipred_score: 0.394
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nhlrc3

Gene ontology

• Biological process: protein polyubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;neutrophil degranulation
• Cellular component: extracellular region;azurophil granule lumen
• Molecular function: ubiquitin protein ligase activity