LRRC34

protein-coding

leucine rich repeat containing 34

Gene summary

Predicted to be involved in cell differentiation. Predicted to act upstream of or within gene expression and telomere maintenance. Predicted to be located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001172779.2

Inheritance

—

ClinVar variants

P:1U:66B:4

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr3:169,793,003-169,812,986

External References & Databases

Ensembl (ENSG00000171757)

Transcript & Mutation Effects

hg38 • Region Span ~20.0 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 LRRC34 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 1

AutismTotal: 1

Primary ciliary dyskinesiaTotal: 1

Joubert syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001172779.2. 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			64 clinvar	4 clinvar		68
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	66	4	0	71

Highest pathogenic variant AF is 0.000009661249

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001172779.2	RefSeq	NP_001166250.1	11	MANE Select
ENST00000446859.7	Ensembl	ENSP00000414635.1	11	MANE Select
NM_001172780.2	RefSeq	NP_001166251.1	9	Standard
NM_001363888.2	RefSeq	NP_001350817.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
cell differentiation

Molecular Function

molecular_function

Cellular Component

cellular_component
nucleolus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000446859
Coding exons: 11
Length: 19559
Individuals with no LoFs: 124979
Homozygous LoFs: 11
Heterozygous LoFs: 737
Defined: 125727
p: 0.00298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.183	225	233	0.966	0.0000113	3014
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.037	0.037	notable
Latino/Admixed American	0.0018	0.0018	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00052	0.00049	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00038	0.00037	rare
South Asian	0.00096	0.00092	rare
Other	0.0025	0.0024	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.000956

Gene Damage Prediction

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