LAD1

protein-coding

ladinin 1

Gene summary

The protein encoded by this gene may be an anchoring filament that is a component of basement membranes. It may contribute to the stability of the association of the epithelial layers with the underlying mesenchyme. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005558.4

Inheritance

—

ClinVar variants

U:18B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr1:201,380,833-201,399,915

External References & Databases

Ensembl (ENSG00000159166)

Transcript & Mutation Effects

hg38 • Region Span ~19.1 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 LAD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005558.4. 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			1 clinvar		3 clinvar	4
missense			10 clinvar	1 clinvar	1 clinvar	12
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	18	1	4	23

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005558.4	RefSeq	NP_005549.2	10	MANE Select
ENST00000391967.7	Ensembl	ENSP00000375829.2	10	MANE Select
ENST00000367313.4	Ensembl	ENSP00000356282.3	10	Standard
ENST00000367313.5	Ensembl	ENSP00000356282.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

structural molecule activity
cadherin binding

Cellular Component

basement membrane
actin cytoskeleton
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000391967
Coding exons: 10
Length: 26365
Individuals with no LoFs: 125671
Homozygous LoFs: 1
Heterozygous LoFs: 76
Defined: 125748
p: 0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.333	284	300	0.946	0.0000182	3276
Missense (PolyPhen)		73	74.165	0.98429		869
Synonymous	1.21	101	118	0.858	0.00000661	1082
Loss of Function	0.274	22	23.4	0.939	0.00000117	293

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00055	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Anchoring filament protein which is a component of the basement membrane zone. {ECO:0000250}.;

Recessive Scores

pRec: 0.365

Intolerance Scores

LoFtool: 0.898
RVIS EVS: 0.85
RVIS percentile EVS: 88.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.387

Gene Damage Prediction

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