LRRC39

leucine rich repeat containing 39

Basic information

Region (hg38): 1:100148447-100178273

Links

ENSG00000122477 ∙ NCBI:127495 ∙ ∙ HGNC:28228 ∙ Uniprot:Q96DD0 ∙ 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 LRRC39 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC39 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	14	1	1

Variants in LRRC39

This is a list of pathogenic ClinVar variants found in the LRRC39 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-100148662-C-A		not specified	Uncertain significance (Feb 17, 2024)
1-100148662-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-100148720-G-T		not specified	Uncertain significance (Jan 31, 2022)
1-100148785-C-T		not specified	Uncertain significance (Dec 14, 2021)
1-100152396-C-T		not specified	Likely benign (Nov 09, 2021)
1-100152445-G-A		not specified	Uncertain significance (Aug 03, 2022)
1-100152498-A-G		not specified	Uncertain significance (Jun 23, 2021)
1-100155074-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-100155081-G-T		not specified	Uncertain significance (Feb 02, 2022)
1-100155157-A-T		not specified	Uncertain significance (Feb 02, 2022)
1-100155168-T-C		not specified	Uncertain significance (Dec 01, 2023)
1-100155186-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-100156206-T-G		not specified	Uncertain significance (Feb 02, 2022)
1-100156229-A-G		not specified	Uncertain significance (Sep 14, 2022)
1-100156278-T-C		not specified	Uncertain significance (Dec 19, 2023)
1-100158232-T-G		not specified	Uncertain significance (May 31, 2023)
1-100158234-T-A		not specified	Uncertain significance (Sep 16, 2021)
1-100158250-A-G		not specified	Uncertain significance (Jan 06, 2023)
1-100158325-T-G		not specified	Uncertain significance (Mar 04, 2024)
1-100159287-G-C		not specified	Uncertain significance (Oct 26, 2022)
1-100159309-A-G		not specified	Uncertain significance (Feb 26, 2024)
1-100159391-G-A			Benign (May 31, 2017)
1-100159405-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-100160485-A-G		not specified	Uncertain significance (Dec 08, 2023)
1-100160498-C-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC39	protein_coding	protein_coding	ENST00000370138	8	29363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000234	0.983	125116	5	621	125742	0.00249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.256	160	169	0.945	0.00000813	2225
Missense in Polyphen		59	63.157	0.93417		843
Synonymous	0.0982	58	59.0	0.984	0.00000273	631
Loss of Function	2.12	9	18.9	0.475	0.00000105	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00366	0.00359
Ashkenazi Jewish	0.00293	0.00288
East Asian	0.0237	0.0232
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000488	0.000484
Middle Eastern	0.0237	0.0232
South Asian	0.00150	0.00144
Other	0.00150	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the sarcomeric M-band which plays a role in myocyte response to biomechanical stress. May regulate expression of other M-band proteins via an SRF-dependent pathway. Important for normal contractile function in heart. {ECO:0000250|UniProtKB:D3ZXS4}.

Recessive Scores

• pRec: 0.0916

Intolerance Scores

• loftool: 0.902
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.351
• hipred: N
• hipred_score: 0.443
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc39

Zebrafish Information Network

• Gene name: lrrc39
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Cellular component: M band
• Molecular function: protein binding