LRRC37A2

protein-coding

leucine rich repeat containing 37 member A2

Gene summary

Predicted to enable ATP binding activity; ATP hydrolysis activity; and metal ion binding activity. Predicted to be involved in SNARE complex disassembly and protein transport. Predicted to be located in cytoplasm and membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001006607.3

Inheritance

—

ClinVar variants

U:131B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr17:46,511,508-46,556,910

External References & Databases

Ensembl (ENSG00000238083)

Transcript & Mutation Effects

hg38 • Region Span ~45.4 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 LRRC37A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001006607.3. 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			131 clinvar	19 clinvar		150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	131	19	0	150

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001006607.3	RefSeq	NP_001006608.2	14	MANE Select
ENST00000576629.6	Ensembl	ENSP00000459551.1	14	MANE Select
NM_001385803.1	RefSeq	NP_001372732.1	14	Standard
ENST00000705813.1	Ensembl	ENSP00000516171.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000576629
Coding exons: 14
Length: 44140
Individuals with no LoFs: 124540
Homozygous LoFs: 2
Heterozygous LoFs: 55
Defined: 124597
p: 0.000229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.376	328	309	1.06	0.0000159	10729
Missense (PolyPhen)		88	83.341	1.0559		2741
Synonymous	0.0535	123	124	0.994	0.00000726	3377
Loss of Function	1.44	14	21.1	0.663	0.00000107	783

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000062	0.000030	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0034	0.0030	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000093	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.0236

Gene Damage Prediction

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