LRRC3C

leucine rich repeat containing 3C

Basic information

Region (hg38): 17:39927731-39944999

Links

ENSG00000204913 ∙ NCBI:100505591 ∙ ∙ HGNC:40034 ∙ Uniprot:A6NJW4 ∙ 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 LRRC3C gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC3C 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in LRRC3C

This is a list of pathogenic ClinVar variants found in the LRRC3C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-39943992-T-C		not specified	Uncertain significance (Dec 08, 2023)
17-39944000-C-A		not specified	Uncertain significance (Jan 10, 2022)
17-39944022-G-A		not specified	Uncertain significance (Nov 03, 2022)
17-39944084-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-39944087-C-T		not specified	Uncertain significance (Jun 21, 2022)
17-39944132-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-39944225-G-A		not specified	Uncertain significance (Jan 18, 2022)
17-39944267-G-T		not specified	Uncertain significance (Oct 04, 2022)
17-39944268-C-T		not specified	Uncertain significance (Apr 08, 2023)
17-39944277-A-T		not specified	Uncertain significance (Dec 12, 2023)
17-39944408-C-T		not specified	Uncertain significance (Dec 01, 2022)
17-39944481-G-A		not specified	Uncertain significance (Nov 07, 2023)
17-39944481-G-T		not specified	Uncertain significance (Jan 24, 2024)
17-39944492-G-A		not specified	Uncertain significance (Jun 22, 2021)
17-39944547-G-T		not specified	Uncertain significance (Dec 20, 2021)
17-39944594-G-A		not specified	Uncertain significance (Feb 22, 2023)
17-39944607-C-T		not specified	Uncertain significance (Dec 28, 2022)
17-39944653-T-G		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC3C	protein_coding	protein_coding	ENST00000377924	2	3274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0292	0.817	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.567	131	151	0.870	0.00000927	1703
Missense in Polyphen		40	46.778	0.85511		582
Synonymous	0.331	62	65.4	0.948	0.00000382	636
Loss of Function	1.10	3	5.87	0.511	2.99e-7	70

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

• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc3c

Gene ontology

• Cellular component: extracellular space;integral component of membrane;extracellular matrix