LRRC34

leucine rich repeat containing 34

Basic information

Region (hg38): 3:169793003-169812986

Links

ENSG00000171757 ∙ NCBI:151827 ∙ OMIM:619037 ∙ HGNC:28408 ∙ Uniprot:Q8IZ02 ∙ 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 LRRC34 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC34 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			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in LRRC34

This is a list of pathogenic ClinVar variants found in the LRRC34 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-169793760-C-T		not specified	Uncertain significance (Dec 14, 2023)
3-169793762-C-T		not specified	Likely benign (Mar 28, 2024)
3-169793769-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-169793771-A-G		not specified	Uncertain significance (Jul 17, 2023)
3-169796223-C-T		not specified	Uncertain significance (Mar 16, 2022)
3-169796763-C-T			Uncertain significance (Sep 09, 2021)
3-169796794-A-G		not specified	Uncertain significance (Nov 07, 2023)
3-169796832-C-A		not specified	Uncertain significance (Sep 16, 2021)
3-169796844-G-A		not specified	Likely benign (Dec 27, 2023)
3-169796875-G-A		not specified	Uncertain significance (Sep 07, 2022)
3-169796889-G-A		not specified	Uncertain significance (Nov 07, 2022)
3-169800679-G-A		not specified	Uncertain significance (Feb 10, 2022)
3-169800710-G-T		not specified	Uncertain significance (Dec 13, 2022)
3-169800751-T-C		not specified	Uncertain significance (Nov 30, 2022)
3-169804064-C-T		not specified	Uncertain significance (Jan 31, 2024)
3-169804079-T-C		not specified	Uncertain significance (Oct 26, 2022)
3-169804175-G-A		not specified	Uncertain significance (Oct 21, 2021)
3-169806847-C-T		Autism	Uncertain significance (-)
3-169806880-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-169807475-T-C		not specified	Uncertain significance (Jun 21, 2023)
3-169807602-C-T		not specified	Uncertain significance (Sep 29, 2022)
3-169807604-A-T		not specified	Likely benign (Dec 06, 2021)
3-169807669-G-C		not specified	Uncertain significance (May 25, 2022)
3-169807669-G-T		not specified	Uncertain significance (Jul 25, 2023)
3-169807675-T-A		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC34	protein_coding	protein_coding	ENST00000446859	11	19559

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.52e-7	0.873	124979	11	737	125727	0.00298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.183	225	233	0.966	0.0000113	3014
Missense in Polyphen		71	74.726	0.95014		1051
Synonymous	0.609	75	82.0	0.915	0.00000393	886
Loss of Function	1.57	13	20.7	0.628	0.00000105	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0389	0.0386
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000523	0.000489
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000375	0.000369
Middle Eastern	0.000523	0.000489
South Asian	0.000960	0.000915
Other	0.00246	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Highly expressed in stem cells where it may be involved in regulation of pluripotency. In embryonic stem cells (ESCs), important for normal expression of the pluripotency regulators POU5F1/OCT4 and KLF4. Also important for expression of the ectodermal marker gene NES and the endodermal marker gene GATA4. Promotes stem cell proliferation in vitro. {ECO:0000250|UniProtKB:Q9DAM1}.

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.0846
• hipred: N
• hipred_score: 0.170
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc34

Gene ontology

• Biological process: biological_process;cell differentiation
• Cellular component: cellular_component;nucleolus;cytoplasm
• Molecular function: molecular_function