NID2

protein-coding

nidogen 2

Gene summary

This gene encodes a member of the nidogen family of basement membrane proteins. This protein is a cell-adhesion protein that binds collagens I and IV and laminin and may be involved in maintaining the structure of the basement membrane.[provided by RefSeq, Jun 2010]

MANE transcript

NM_007361.4

Inheritance

—

ClinVar variants

U:261B:38

Top phenotype

NID2-related condition

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr14:52,004,809-52,069,059

External References & Databases

Ensembl (ENSG00000087303)

Transcript & Mutation Effects

hg38 • Region Span ~64.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NID2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 262

not providedTotal: 25

NID2-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007361.4. 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	8 clinvar	4 clinvar	15
missense			254 clinvar	20 clinvar	6 clinvar	280
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	261	28	10	299

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007361.4	RefSeq	NP_031387.3	22	MANE Select
ENST00000216286.10	Ensembl	ENSP00000216286.4	22	MANE Select
ENST00000556572.1	Ensembl	ENSP00000452190.1	13	Standard
ENST00001111464.1	Ensembl	ENSP00000781269.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Laminin interactions
Extracellular matrix organization

Biological Process

cell adhesion
cell-matrix adhesion
extracellular matrix organization
basement membrane organization

Molecular Function

extracellular matrix structural constituent
calcium ion binding
protein binding
collagen binding

Cellular Component

extracellular region
basement membrane
plasma membrane
collagen-containing extracellular matrix
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216286
Coding exons: 22
Length: 64192
Individuals with no LoFs: 125679
Homozygous LoFs: 0
Heterozygous LoFs: 69
Defined: 125748
p: 0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.250	826	806	1.02	0.0000448	8892
Missense (PolyPhen)		245	280.57	0.87322		3128
Synonymous	-1.30	360	330	1.09	0.0000195	2789
Loss of Function	4.45	26	64.6	0.403	0.00000315	730

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00027	0.00026	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cell adhesion glycoprotein which is widely distributed in basement membranes. Binds to collagens I and IV, to perlecan and to laminin 1. Does not bind fibulins. It probably has a role in cell-extracellular matrix interactions.;

Recessive Scores

pRec: 0.207

Intolerance Scores

LoFtool: 0.113
RVIS EVS: 3.6
RVIS percentile EVS: 99.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.577

Gene Damage Prediction

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