HRNR

protein-coding

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

Gene summary

Predicted to enable calcium ion binding activity and transition metal ion binding activity. Involved in cell envelope organization and establishment of skin barrier. Located in cornified envelope; keratohyalin granule; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001009931.3

Inheritance

—

ClinVar variants

U:13B:55

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 1.86

Max pathogenic AF

—

Genomic locus

chr1:152,212,076-152,224,193

External References & Databases

Ensembl (ENSG00000197915)

Transcript & Mutation Effects

hg38 • Region Span ~12.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HRNR variants in ClinVar

5 Conditions Cataloged

not providedTotal: 56

not specifiedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

AutismTotal: 1

Epidermolysis bullosa simplex with nail dystrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001009931.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	44 clinvar		45
missense			10 clinvar	5 clinvar	3 clinvar	18
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift			1 clinvar	2 clinvar		3
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	52	3	68

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001009931.3	RefSeq	NP_001009931.1	2	MANE Select
ENST00000368801.4	Ensembl	ENSP00000357791.3	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

keratinization
cell envelope organization
neutrophil degranulation
establishment of skin barrier

Molecular Function

calcium ion binding
structural constituent of epidermis
transition metal ion binding

Cellular Component

cornified envelope
extracellular region
nucleus
cytoplasm
azurophil granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368801
Coding exons: 2
Length: 12112
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125724
p: 0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-11.5	2023	998	2.03	0.0000605	16790
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000028	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the epidermal cornified cell envelopes. {ECO:0000269|PubMed:21282207}.;

Recessive Scores

pRec: 0.109

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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