LRRC37A

leucine rich repeat containing 37A

Basic information

Region (hg38): 17:46292733-46338077

Links

ENSG00000176681 ∙ NCBI:9884 ∙ OMIM:616555 ∙ HGNC:29069 ∙ Uniprot:A6NMS7 ∙ 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 LRRC37A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC37A 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			40	10		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	10	1

Variants in LRRC37A

This is a list of pathogenic ClinVar variants found in the LRRC37A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-46295307-G-C		not specified	Uncertain significance (Apr 13, 2022)
17-46297246-A-G		not specified	Uncertain significance (Jan 24, 2023)
17-46297258-C-G		not specified	Uncertain significance (Apr 04, 2024)
17-46297291-C-T		not specified	Uncertain significance (Feb 23, 2023)
17-46297322-A-T		not specified	Uncertain significance (Sep 14, 2022)
17-46297344-A-G		not specified	Benign (Mar 29, 2016)
17-46297432-A-G		not specified	Uncertain significance (Mar 08, 2024)
17-46297453-G-A		not specified	Uncertain significance (Apr 28, 2022)
17-46297456-C-T		not specified	Uncertain significance (Jan 20, 2023)
17-46297468-C-T		not specified	Uncertain significance (Jul 06, 2021)
17-46297471-G-C		not specified	Likely benign (Dec 21, 2023)
17-46297478-C-G		not specified	Uncertain significance (Jun 10, 2024)
17-46297493-T-C		not specified	Uncertain significance (Jul 27, 2021)
17-46297514-C-T		not specified	Uncertain significance (Jun 13, 2024)
17-46297520-A-T		not specified	Uncertain significance (Nov 29, 2023)
17-46297529-C-G		not specified	Uncertain significance (Aug 08, 2022)
17-46297531-G-A		not specified	Likely benign (Jan 03, 2024)
17-46297604-C-T		not specified	Uncertain significance (Nov 21, 2022)
17-46297613-G-A		not specified	Likely benign (Jun 30, 2022)
17-46297705-C-T		not specified	Likely benign (Oct 26, 2021)
17-46305526-A-T		not specified	Uncertain significance (Dec 28, 2022)
17-46305558-C-T		not specified	Likely benign (Nov 09, 2021)
17-46322332-C-A		not specified	Uncertain significance (May 08, 2023)
17-46322338-C-A		not specified	Uncertain significance (Oct 05, 2021)
17-46322967-C-G		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC37A	protein_coding	protein_coding	ENST00000320254	14	45062

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000543	0.900	120270	0	3	120273	0.0000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	150	198	0.758	0.0000102	10880
Missense in Polyphen		18	28.015	0.64252		1584
Synonymous	1.69	61	80.3	0.760	0.00000484	3428
Loss of Function	1.46	7	12.6	0.556	5.76e-7	791

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000136	0.000130
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000919	0.00000902
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0355
• hipred: N
• hipred_score: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: 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