LRCH3

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	6 clinvar		7
missense			105 clinvar	6 clinvar		111
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	114	12	0	126

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001365715.1	RefSeq	NP_001352644.1	21	MANE Select
ENST00000425562.7	Ensembl	ENSP00000393579.2	21	MANE Select
NM_001363887.1	RefSeq	NP_001350816.1	21	Standard
NM_001365716.1	RefSeq	NP_001352645.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

extracellular region
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334859
Coding exons: 19
Length: 97211
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 108
Defined: 125748
p: 0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.278	371	386	0.960	0.0000204	4552
Missense (PolyPhen)		115	128.36	0.89591		1478
Synonymous	0.301	145	150	0.969	0.00000808	1441
Loss of Function	2.54	25	43.0	0.582	0.00000239	485

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00043	rare
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00042	0.00041	rare
South Asian	0.00052	0.00052	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0981

Intolerance Scores

LoFtool: 0.842
RVIS EVS: -0.53
RVIS percentile EVS: 20.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

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