LRRC37A3

leucine rich repeat containing 37 member A3

Basic information

Region (hg38): 17:64854129-64919480

Links

ENSG00000176809 ∙ NCBI:374819 ∙ OMIM:616557 ∙ HGNC:32427 ∙ Uniprot:O60309 ∙ 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 LRRC37A3 gene.

• Inborn genetic diseases (86 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC37A3 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				3	3	6
missense			75	11	2	88
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	75	15	5

Variants in LRRC37A3

This is a list of pathogenic ClinVar variants found in the LRRC37A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-64855876-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-64858783-A-G		not specified	Uncertain significance (Dec 07, 2021)
17-64858822-G-A		not specified	Uncertain significance (Feb 11, 2022)
17-64858834-G-A		not specified	Uncertain significance (Feb 27, 2024)
17-64858856-A-G		not specified	Uncertain significance (Sep 17, 2021)
17-64859494-T-A		not specified	Uncertain significance (Oct 05, 2023)
17-64859510-A-G		not specified	Uncertain significance (Jul 19, 2023)
17-64859522-C-A		not specified	Uncertain significance (Dec 18, 2023)
17-64859581-C-T		not specified	Uncertain significance (Sep 27, 2022)
17-64859594-C-T		not specified	Likely benign (Mar 30, 2022)
17-64859658-A-T		not specified	Uncertain significance (Sep 27, 2022)
17-64859787-G-C		not specified	Uncertain significance (May 15, 2023)
17-64859799-G-A			Benign (Dec 31, 2019)
17-64859813-A-G		not specified	Uncertain significance (Apr 12, 2022)
17-64859864-C-T		not specified	Uncertain significance (Sep 22, 2023)
17-64859887-T-C		not specified	Uncertain significance (Nov 02, 2023)
17-64859888-T-C		not specified	Uncertain significance (Mar 06, 2023)
17-64859938-A-G		not specified	Uncertain significance (Feb 15, 2023)
17-64859952-T-G		not specified	Uncertain significance (Apr 07, 2022)
17-64859955-A-C		not specified	Uncertain significance (Sep 23, 2023)
17-64859995-T-C		not specified	Uncertain significance (Jan 23, 2024)
17-64860028-A-C		not specified	Uncertain significance (Nov 29, 2023)
17-64860033-A-G			Benign (Dec 31, 2019)
17-64860035-G-A			Benign (Dec 31, 2019)
17-64860117-C-T			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC37A3	protein_coding	protein_coding	ENST00000584306	12	65169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.09e-10	0.978	125656	0	86	125742	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.120	555	547	1.01	0.0000298	10422
Missense in Polyphen		79	90.508	0.87285		2026
Synonymous	-0.404	233	225	1.03	0.0000139	3324
Loss of Function	2.27	21	35.7	0.589	0.00000170	726

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00121
Ashkenazi Jewish	0.000215	0.000198
East Asian	0.0000547	0.0000544
Finnish	0.000958	0.000924
European (Non-Finnish)	0.000308	0.000281
Middle Eastern	0.0000547	0.0000544
South Asian	0.000269	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.172

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc37a

Gene ontology

• Cellular component: integral component of membrane