LRRC53

leucine rich repeat containing 53

Basic information

Region (hg38): 1:74469376-74512611

Links

ENSG00000162621 ∙ NCBI:105378803 ∙ ∙ HGNC:25255 ∙ Uniprot:A6NM62 ∙ 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 LRRC53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC53 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			1	1		2
nonsense			1			1
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		2	53	35	7	97
Total	0	2	55	38	7

Variants in LRRC53

This is a list of pathogenic ClinVar variants found in the LRRC53 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-74470408-C-T			Likely benign (Nov 01, 2022)
1-74470900-T-C			Likely benign (Jan 01, 2025)
1-74470992-G-A		Atrial conduction disease	Uncertain significance (Feb 15, 2023)
1-74471075-C-CTCAG		Atrial conduction disease	Uncertain significance (Jun 10, 2021)
1-74472172-ATCT-A			Likely benign (Sep 01, 2022)
1-74475689-A-G			Likely benign (Jul 01, 2022)
1-74489152-ATTCTTAAGGGAAAAAAG-A			Uncertain significance (Dec 18, 2023)
1-74489169-G-T			Likely benign (Feb 10, 2023)
1-74489172-C-A			Likely benign (May 13, 2024)
1-74489172-C-T			Likely benign (Dec 19, 2024)
1-74489172-CT-C			Benign (Mar 12, 2022)
1-74489172-C-CT			Benign (Feb 04, 2025)
1-74489186-C-G			Uncertain significance (Jun 21, 2021)
1-74489188-G-A			Uncertain significance (Jun 11, 2024)
1-74489190-G-C			Uncertain significance (Apr 16, 2022)
1-74489191-A-G			Likely benign (Aug 27, 2024)
1-74489195-C-A		Inborn genetic diseases • Atrial conduction disease	Conflicting classifications of pathogenicity (Jan 28, 2025)
1-74489197-C-T			Likely benign (May 14, 2024)
1-74489198-G-A			Uncertain significance (Nov 21, 2024)
1-74489203-T-C			Likely benign (Apr 25, 2022)
1-74489207-G-A			Uncertain significance (Oct 29, 2024)
1-74489207-G-C			Uncertain significance (Sep 02, 2021)
1-74489216-A-G		not specified • TNNI3K-related disorder	Likely benign (Apr 09, 2025)
1-74489217-T-C			Uncertain significance (Dec 17, 2024)
1-74489223-T-TA		See cases • Atrial conduction disease	Uncertain significance (Jan 29, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC53	protein_coding	protein_coding	ENST00000294635	4	42737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-10	0.109	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.893	231	273	0.848	0.0000139	8182
Missense in Polyphen		42	58.772	0.71463		1243
Synonymous	1.72	92	115	0.797	0.00000632	2373
Loss of Function	0.333	16	17.5	0.914	0.00000101	509

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

Haploinsufficiency Scores

• pHI: 0.502
• ghis: 0.394

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0293

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane