LINS1

lines homolog 1

Basic information

Region (hg38): 15:100559369-100603230

Previous symbols: [ "LINS", "MRT27" ]

Links

ENSG00000140471 ∙ NCBI:55180 ∙ OMIM:610350 ∙ HGNC:30922 ∙ Uniprot:Q8NG48 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal recessive 27 (Strong), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• complex neurodevelopmental disorder (Definitive), mode of inheritance: AR
• intellectual disability, autosomal recessive 27 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 27	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	21937992; 23773660

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LINS1 gene.

• Inborn_genetic_diseases (79 variants)
• not_provided (61 variants)
• Intellectual_disability,_autosomal_recessive_27 (43 variants)
• not_specified (22 variants)
• LINS1-related_disorder (6 variants)
• Autism (1 variants)
• Microcephaly (1 variants)
• Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040616.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				36		36
missense		2	64	13	1	80
nonsense	3	6				9
start loss						0
frameshift	6	14	3			23
splice donor/acceptor (+/-2bp)	1	4				5
Total	10	26	67	49	1

Highest pathogenic variant AF is 0.000077492565

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINS1	protein_coding	protein_coding	ENST00000314742	6	43862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.37e-7	0.906	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.684	427	389	1.10	0.0000189	5010
Missense in Polyphen		104	100.13	1.0387		1453
Synonymous	0.0262	143	143	0.997	0.00000733	1415
Loss of Function	1.70	14	22.8	0.615	9.52e-7	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000151
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000329	0.000308
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0873

Intolerance Scores

• rvis_EVS: 1.03
• rvis_percentile_EVS: 91.09

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.123
• ghis: 0.470

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0978

Mouse Genome Informatics

• Gene name: Lins1

Gene ontology

• Biological process: cognition