NID1

protein-coding

nidogen 1

Gene summary

This gene encodes a member of the nidogen family of basement membrane glycoproteins. The protein interacts with several other components of basement membranes, and may play a role in cell interactions with the extracellular matrix. [provided by RefSeq, Jul 2008]

Previous symbols:

MANE transcript

NM_002508.3

Inheritance

ClinVar variants

P:2U:208B:37

Top phenotype

central nervous system malformation

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr1:235,975,830-236,065,109

External References & Databases

Ensembl (ENSG00000116962)

Transcript & Mutation Effects

hg38 • Region Span ~89.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

central nervous system malformationSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0020022

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NID1 variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 203

not providedTotal: 41

HemiparesisTotal: 1

HydrocephalusTotal: 1

Focal epilepsyTotal: 1

Variant of unknown significanceTotal: 1

Cerebellar dysfunction with variable cognitive and behavioral abnormalitiesTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002508.3. 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			3 clinvar	9 clinvar	8 clinvar	20
missense			197 clinvar	11 clinvar	9 clinvar	217
nonsense			2 clinvar			2
start loss		1 clinvar				1
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	4 clinvar			5
Total	0	2	208	20	17	247

Highest pathogenic variant AF is 0.000013145614

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002508.3	RefSeq	NP_002499.2	20	MANE Select
ENST00000264187.7	Ensembl	ENSP00000264187.6	20	MANE Select
ENST00000366595.7	Ensembl	ENSP00000355554.3	17	Standard
ENST00000366595.8	Ensembl	ENSP00000355554.3	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Laminin interactions
Extracellular matrix organization
Degradation of the extracellular matrix
Beta1 integrin cell surface interactions

Biological Process

cell-matrix adhesion
positive regulation of cell-substrate adhesion
extracellular matrix organization
glomerular basement membrane development
basement membrane organization

Molecular Function

extracellular matrix structural constituent
calcium ion binding
collagen binding
laminin binding
laminin-1 binding

Cellular Component

extracellular region
basement membrane
collagen-containing extracellular matrix
extracellular exosome
cell periphery

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264187
Coding exons: 20
Length: 89333
Individuals with no LoFs: 125685
Homozygous LoFs: 1
Heterozygous LoFs: 62
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.482	743	781	0.951	0.0000489	8076
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00049	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.351

Intolerance Scores

LoFtool: 0.0768
RVIS EVS: 0.45
RVIS percentile EVS: 77.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.862

Gene Damage Prediction

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