LRRC31

leucine rich repeat containing 31

Basic information

Region (hg38): 3:169839171-169869935

Links

ENSG00000114248 ∙ NCBI:79782 ∙ ∙ HGNC:26261 ∙ Uniprot:Q6UY01 ∙ 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 LRRC31 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC31 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in LRRC31

This is a list of pathogenic ClinVar variants found in the LRRC31 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-169839992-C-T		not specified	Uncertain significance (Aug 16, 2021)
3-169840011-T-G		not specified	Uncertain significance (Jan 26, 2022)
3-169840131-G-A		not specified	Uncertain significance (Mar 28, 2023)
3-169840209-G-A		not specified	Likely benign (Feb 10, 2022)
3-169840265-A-G		not specified	Uncertain significance (May 24, 2023)
3-169840310-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-169848248-T-C		not specified	Uncertain significance (Mar 17, 2023)
3-169851639-C-G		not specified	Uncertain significance (Feb 14, 2023)
3-169851748-C-T		not specified	Uncertain significance (Jul 12, 2022)
3-169851754-C-T		not specified	Uncertain significance (Jul 14, 2021)
3-169851774-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-169854826-G-T		not specified	Uncertain significance (Jun 24, 2022)
3-169856456-T-C		not specified	Uncertain significance (Dec 30, 2023)
3-169856736-G-C		not specified	Uncertain significance (Dec 30, 2023)
3-169856752-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-169856864-A-G		not specified	Likely benign (Dec 06, 2021)
3-169860588-G-C		not specified	Uncertain significance (May 17, 2023)
3-169860600-C-A		not specified	Uncertain significance (Feb 05, 2024)
3-169860611-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-169860644-G-A		not specified	Uncertain significance (Dec 06, 2021)
3-169860683-G-A		not specified	Uncertain significance (Oct 03, 2023)
3-169860708-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-169861688-C-T		not specified	Uncertain significance (Nov 22, 2021)
3-169861700-C-G		not specified	Likely benign (Jan 04, 2024)
3-169861715-C-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC31	protein_coding	protein_coding	ENST00000316428	9	30752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000200	0.974	123734	10	1054	124798	0.00427

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.150	283	276	1.03	0.0000131	3601
Missense in Polyphen		73	69.601	1.0488		966
Synonymous	-0.198	113	110	1.02	0.00000580	1053
Loss of Function	2.06	13	23.9	0.545	0.00000123	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0288	0.0288
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000280	0.000278
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.000327	0.000327
Middle Eastern	0.000280	0.000278
South Asian	0.00131	0.00131
Other	0.00316	0.00314

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.796
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.84

Haploinsufficiency Scores

• pHI: 0.0850
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc31