LRRC73

Gene

leucine rich repeat containing 73

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C6orf154

MANE transcript

NM_001012974.4

Inheritance

—

ClinVar variants

U:37

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr6:43,506,968-43,510,346

External References & Databases

Ensembl (ENSG00000204052)

Transcript & Mutation Effects

hg38 • Region Span ~3.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRRC73 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012974.4. Only rare variants are included.

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						0
missense			37 clinvar			37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	0	0	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001012974.4	RefSeq	NP_001012992.1	6	MANE Select
ENST00000372441.2	Ensembl	ENSP00000361518.1	6	MANE Select
NM_001271882.2	RefSeq	NP_001258811.1	5	Standard
ENST00000899667.1	Ensembl	ENSP00000569726.1	5	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372441
Coding exons: 6
Length: 3718
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125710
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.62	124	186	0.666	0.00000962	2009
Missense (PolyPhen)		29	40.496	0.71612		481
Synonymous	-1.44	97	80.6	1.20	0.00000420	691
Loss of Function	2.01	4	11.3	0.354	4.81e-7	130

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 56.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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