HRNR

hornerin, the group of EF-hand domain containing|S100 fused type protein family

Basic information

Region (hg38): 1:152212075-152224193

Links

ENSG00000197915 ∙ NCBI:388697 ∙ OMIM:616293 ∙ HGNC:20846 ∙ Uniprot:Q86YZ3 ∙ 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 HRNR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HRNR 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				20	1	21
missense			3	3	3	9
nonsense			1	1		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	24	4

Variants in HRNR

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

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

Position	Type	Phenotype	Significance	ClinVar
1-152213255-A-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-152213599-C-G			Benign (Mar 01, 2022)
1-152214009-C-T			Likely benign (Nov 01, 2023)
1-152214030-G-T			Likely benign (Mar 01, 2023)
1-152214345-A-G			Likely benign (Jul 01, 2023)
1-152214519-G-A			Likely benign (Sep 01, 2022)
1-152214627-G-T			Likely benign (Nov 01, 2022)
1-152215077-G-A			Likely benign (Sep 01, 2022)
1-152215356-A-G			Likely benign (Oct 01, 2022)
1-152215365-G-T			Likely benign (Dec 01, 2022)
1-152215572-A-G			Likely benign (Dec 01, 2022)
1-152218176-A-G			Likely benign (Aug 01, 2023)
1-152218397-G-A			Likely benign (Aug 01, 2023)
1-152218471-C-T			Likely benign (Nov 01, 2022)
1-152218588-T-C		Epidermolysis bullosa simplex with nail dystrophy	Uncertain significance (Oct 01, 2022)
1-152218606-C-G			Likely benign (Jan 01, 2023)
1-152218749-G-A			Likely benign (Jan 01, 2023)
1-152219182-C-A			Likely benign (Mar 01, 2023)
1-152219233-C-G			Benign (Mar 04, 2019)
1-152219304-A-C			Likely benign (Mar 01, 2023)
1-152219403-G-A			Benign (Mar 04, 2019)
1-152219490-G-C			Uncertain significance (Jul 01, 2019)
1-152219666-C-G			Uncertain significance (Jul 01, 2019)
1-152219829-G-A			Likely benign (Oct 01, 2022)
1-152219995-C-T			Benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HRNR	protein_coding	protein_coding	ENST00000368801	2	12112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000426	0.249	125709	0	15	125724	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-11.5	2023	998	2.03	0.0000605	16790
Missense in Polyphen		64	50.794	1.26		694
Synonymous	-11.4	720	422	1.71	0.0000270	5904
Loss of Function	-1.17	4	2.15	1.86	9.13e-8	24

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000348	0.000348
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000281	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the epidermal cornified cell envelopes. {ECO:0000269|PubMed:21282207}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.301

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hrnr

Gene ontology

• Biological process: keratinization;cell envelope organization;neutrophil degranulation;establishment of skin barrier
• Cellular component: cornified envelope;extracellular region;nucleus;cytoplasm;azurophil granule lumen;keratohyalin granule;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: calcium ion binding;structural constituent of epidermis;transition metal ion binding