NID1

nidogen 1

Basic information

Region (hg38): 1:235975830-236065109

Previous symbols: [ "NID" ]

Links

ENSG00000116962 ∙ NCBI:4811 ∙ OMIM:131390 ∙ HGNC:7821 ∙ Uniprot:P14543 ∙ 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 NID1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NID1 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				7	12	19
missense			83	9	13	105
nonsense			1			1
start loss		1				1
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					5	5
non coding					41	41
Total	0	1	85	16	66

Variants in NID1

This is a list of pathogenic ClinVar variants found in the NID1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-235977874-T-C			Benign (Nov 12, 2018)
1-235977919-G-T		not specified	Uncertain significance (Apr 09, 2024)
1-235977930-T-TG			Uncertain significance (Jun 27, 2017)
1-235977934-G-A			Benign (May 18, 2018)
1-235977953-T-C		not specified	Uncertain significance (Apr 22, 2022)
1-235977959-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-235977973-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-235978953-T-G			Benign (Nov 12, 2018)
1-235979031-A-T		not specified	Uncertain significance (May 11, 2022)
1-235979111-C-T			Benign (Jan 01, 2023)
1-235979265-T-C			Benign (Nov 12, 2018)
1-235979270-C-G			Benign (Nov 12, 2018)
1-235979844-G-C			Benign (Jun 08, 2018)
1-235979860-C-T		not specified	Likely benign (May 31, 2024)
1-235979907-T-A		not specified	Uncertain significance (Oct 26, 2021)
1-235979936-C-A		not specified	Uncertain significance (Mar 04, 2024)
1-235980002-C-CA			Benign (Nov 12, 2018)
1-235980495-C-T		Hydrocephalus;Hemiparesis;Focal epilepsy	Likely pathogenic (Dec 01, 2014)
1-235980561-T-A		not specified	Uncertain significance (Oct 25, 2022)
1-235980579-C-G		not specified	Uncertain significance (Apr 19, 2023)
1-235980587-C-T			Likely benign (Jul 17, 2018)
1-235980598-T-C		not specified	Uncertain significance (Oct 06, 2022)
1-235980961-T-C			Benign (Nov 12, 2018)
1-235981454-C-A			Benign (Nov 12, 2018)
1-235981619-G-T			Benign (Nov 08, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NID1	protein_coding	protein_coding	ENST00000264187	20	89333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.22e-12	1.00	125685	1	62	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.482	743	781	0.951	0.0000489	8076
Missense in Polyphen		194	244.97	0.79193		2536
Synonymous	-0.204	347	342	1.01	0.0000244	2540
Loss of Function	3.78	29	60.8	0.477	0.00000342	627

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000815	0.000814
Ashkenazi Jewish	0.00	0.00
East Asian	0.000436	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000436	0.000435
South Asian	0.000490	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfated glycoprotein widely distributed in basement membranes and tightly associated with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell- extracellular matrix interactions.
• Pathway: Laminin interactions;Extracellular matrix organization;Degradation of the extracellular matrix;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.351

Intolerance Scores

• loftool: 0.0768
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.93

Haploinsufficiency Scores

• pHI: 0.785
• hipred: Y
• hipred_score: 0.602
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nid1
• Phenotype: cellular phenotype; muscle phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cell-matrix adhesion;positive regulation of cell-substrate adhesion;extracellular matrix organization;glomerular basement membrane development;basement membrane organization
• Cellular component: extracellular region;basement membrane;collagen-containing extracellular matrix;extracellular exosome;cell periphery
• Molecular function: extracellular matrix structural constituent;calcium ion binding;collagen binding;laminin binding;laminin-1 binding;proteoglycan binding