LAD1

ladinin 1

Basic information

Region (hg38): 1:201380833-201399915

Links

ENSG00000159166 ∙ NCBI:3898 ∙ OMIM:602314 ∙ HGNC:6472 ∙ Uniprot:O00515 ∙ 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 LAD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAD1 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					3	3
missense			8		1	9
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	5

Variants in LAD1

This is a list of pathogenic ClinVar variants found in the LAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201383381-A-C		not specified	Uncertain significance (Aug 02, 2021)
1-201384813-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-201385730-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-201386371-C-T			Benign (Aug 17, 2018)
1-201386497-C-T			Benign (Apr 09, 2018)
1-201386770-G-A			Benign (Apr 06, 2018)
1-201386876-ACC-A			Benign (Aug 27, 2018)
1-201387170-C-T			Benign (Aug 23, 2018)
1-201389183-G-T		not specified	Uncertain significance (Aug 16, 2021)
1-201389199-A-C		not specified	Uncertain significance (Oct 12, 2021)
1-201389215-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-201389239-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-201399279-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAD1	protein_coding	protein_coding	ENST00000391967	10	26365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.78e-14	0.0284	125671	1	76	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.333	284	300	0.946	0.0000182	3276
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000720	0.000714
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000347	0.000343
Middle Eastern	0.000163	0.000163
South Asian	0.000548	0.000425
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.146
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lad1

Gene ontology

• Cellular component: basement membrane;actin cytoskeleton;extracellular exosome
• Molecular function: structural molecule activity;cadherin binding