LDLRAD2

protein-coding

low density lipoprotein receptor class A domain containing 2

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001013693.3

Inheritance

—

ClinVar variants

P:1U:57B:2

Top phenotype

Schwartz-Jampel syndrome type 1

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr1:21,812,265-21,825,225

External References & Databases

Ensembl (ENSG00000187942)

Transcript & Mutation Effects

hg38 • Region Span ~13.0 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 LDLRAD2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 1

Schwartz-Jampel syndrome type 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001013693.3. 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			57 clinvar	2 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	1	0	57	2	0	60

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001013693.3	RefSeq	NP_001013715.2	5	MANE Select
ENST00000344642.7	Ensembl	ENSP00000340988.2	5	MANE Select
ENST00000543870.1	Ensembl	ENSP00000444097.1	5	Standard
ENST00000543870.2	Ensembl	ENSP00000444097.1	5	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: ENST00000344642
Coding exons: 5
Length: 12957
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125745
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.192	161	154	1.04	0.00000784	1680
Missense (PolyPhen)		37	36.937	1.0017		452
Synonymous	-0.651	81	73.9	1.10	0.00000392	611
Loss of Function	1.02	7	10.6	0.662	4.53e-7	113

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00015	0.00013	rare
South Asian	0.00056	0.00056	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.462
RVIS EVS: 0.01
RVIS percentile EVS: 54.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0199

Gene Damage Prediction

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