LRRC37A2

leucine rich repeat containing 37 member A2

Basic information

Region (hg38): 17:46511507-46556910

Links

ENSG00000238083 ∙ NCBI:474170 ∙ OMIM:616556 ∙ HGNC:32404 ∙ Uniprot:A6NM11 ∙ 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 LRRC37A2 gene.

• Inborn genetic diseases (51 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC37A2 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			42	8		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	44	8	0

Variants in LRRC37A2

This is a list of pathogenic ClinVar variants found in the LRRC37A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-46512741-T-C		not specified	Likely benign (Jan 17, 2024)
17-46512762-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-46512809-C-G		not specified	Uncertain significance (Jan 23, 2023)
17-46512917-C-T		not specified	Likely benign (Apr 13, 2023)
17-46512972-T-C		not specified	Uncertain significance (Nov 10, 2022)
17-46513017-C-T		not specified	Likely benign (Jul 25, 2023)
17-46513035-C-A		not specified	Uncertain significance (Aug 08, 2022)
17-46513160-C-G		not specified	Uncertain significance (May 25, 2022)
17-46513308-T-G		not specified	Uncertain significance (Dec 09, 2023)
17-46513311-G-A		not specified	Uncertain significance (Oct 05, 2021)
17-46513422-C-T		not specified	Likely benign (Jun 22, 2021)
17-46513452-C-T		not specified	Uncertain significance (Jun 30, 2022)
17-46514691-G-A		not specified	Likely benign (Jun 30, 2022)
17-46514949-C-T		not specified	Uncertain significance (May 17, 2023)
17-46514987-C-T		not specified	Uncertain significance (Mar 02, 2023)
17-46515039-G-A		not specified	Likely benign (Jan 17, 2024)
17-46515041-C-A		not specified	Uncertain significance (Feb 10, 2022)
17-46515178-C-G		not specified	Likely benign (Jul 21, 2021)
17-46517231-G-C		not specified	Uncertain significance (Jul 21, 2021)
17-46517428-G-C		not specified	Uncertain significance (Apr 18, 2023)
17-46538392-C-T			Uncertain significance (Jun 01, 2022)
17-46540856-A-C		not specified	Uncertain significance (Jan 23, 2024)
17-46540856-A-G		not specified	Uncertain significance (Sep 14, 2022)
17-46546274-G-A		not specified	Uncertain significance (Nov 05, 2021)
17-46546292-T-C		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC37A2	protein_coding	protein_coding	ENST00000576629	14	44140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-7	0.801	124540	2	55	124597	0.000229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.376	328	309	1.06	0.0000159	10729
Missense in Polyphen		88	83.341	1.0559		2741
Synonymous	0.0535	123	124	0.994	0.00000726	3377
Loss of Function	1.44	14	21.1	0.663	0.00000107	783

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000623	0.0000623
Ashkenazi Jewish	0.00	0.00
East Asian	0.00335	0.00302
Finnish	0.00	0.00
European (Non-Finnish)	0.00000927	0.00000884
Middle Eastern	0.00335	0.00302
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0236

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