LINS1

lines homolog 1

Basic information

Region (hg38): 15:100559368-100603230

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

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 (91 variants)
• not provided (81 variants)
• Intellectual disability, autosomal recessive 27 (34 variants)
• not specified (20 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.

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		1	1	29	5	36
missense			58	8	6	72
nonsense	1	5				6
start loss						0
frameshift	1	9	2	1		13
inframe indel			5			5
splice donor/acceptor (+/-2bp)	1	2				3
splice region			2			2
non coding			1		26	27
Total	3	17	67	38	37

Highest pathogenic variant AF is 0.0000329

Variants in LINS1

This is a list of pathogenic ClinVar variants found in the LINS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-100568921-T-C			Benign (Jun 19, 2021)
15-100569017-G-T			Benign (Jun 19, 2021)
15-100569022-A-G			Benign (Jun 19, 2021)
15-100569038-T-C			Benign (Jun 19, 2021)
15-100569049-A-G			Benign (Jun 19, 2021)
15-100569071-T-C			Benign (Jun 19, 2021)
15-100569122-CAAAA-C			Benign (Jun 20, 2021)
15-100569122-C-CA			Benign (Jun 19, 2021)
15-100569122-C-CAA			Benign (Jun 19, 2021)
15-100569153-A-G			Benign (Jun 19, 2021)
15-100569187-C-T			Benign (Jun 20, 2021)
15-100569242-A-T		Intellectual disability, autosomal recessive 27 • Inborn genetic diseases	Conflicting classifications of pathogenicity (May 03, 2020)
15-100569276-T-C			Uncertain significance (Mar 18, 2014)
15-100569283-TAAC-T		Intellectual disability, autosomal recessive 27	Uncertain significance (Nov 25, 2021)
15-100569327-T-A		Intellectual disability, autosomal recessive 27	Likely pathogenic (Mar 25, 2024)
15-100569329-T-C		Inborn genetic diseases	Uncertain significance (Oct 04, 2018)
15-100569334-C-T		Inborn genetic diseases	Likely benign (Jul 28, 2019)
15-100569339-G-A		Inborn genetic diseases	Uncertain significance (Jul 17, 2018)
15-100569349-A-G		Inborn genetic diseases	Likely benign (May 20, 2019)
15-100569391-T-A		Inborn genetic diseases	Likely benign (Aug 21, 2019)
15-100569393-C-T		not specified • Inborn genetic diseases • LINS1-related disorder	Benign/Likely benign (Feb 04, 2022)
15-100569405-C-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
15-100569415-T-C			Likely benign (May 18, 2018)
15-100569422-A-C		Intellectual disability, autosomal recessive 27	Uncertain significance (Nov 02, 2021)
15-100569432-C-A		Inborn genetic diseases	Uncertain significance (Aug 19, 2019)

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