NID2

nidogen 2

Basic information

Region (hg38): 14:52004809-52069059

Links

ENSG00000087303 ∙ NCBI:22795 ∙ OMIM:605399 ∙ HGNC:13389 ∙ Uniprot:Q14112 ∙ 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 NID2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NID2 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				4	4	8
missense			94	12	6	112
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	94	16	11

Variants in NID2

This is a list of pathogenic ClinVar variants found in the NID2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-52005746-A-G		not specified	Uncertain significance (Sep 27, 2022)
14-52005784-C-G		not specified	Uncertain significance (Dec 14, 2021)
14-52005803-C-G		not specified	Uncertain significance (Jun 28, 2024)
14-52006562-G-A			Likely benign (May 14, 2018)
14-52006594-T-G		not specified	Uncertain significance (Nov 10, 2024)
14-52006612-A-G		not specified	Uncertain significance (Oct 04, 2024)
14-52007912-A-C		not specified	Uncertain significance (Nov 10, 2024)
14-52007949-G-C		not specified	Uncertain significance (Oct 12, 2022)
14-52010898-T-C		not specified	Uncertain significance (Jul 31, 2024)
14-52010903-C-T		not specified	Uncertain significance (Nov 09, 2024)
14-52010917-A-G			Benign/Likely benign (Oct 01, 2022)
14-52010935-C-G		not specified	Uncertain significance (Jul 19, 2022)
14-52010952-C-A		not specified	Uncertain significance (Aug 30, 2022)
14-52010961-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-52010990-G-A		not specified	Uncertain significance (Jan 02, 2024)
14-52011009-G-A		not specified	Uncertain significance (Dec 27, 2023)
14-52011011-A-G		not specified	Uncertain significance (Nov 14, 2023)
14-52011020-A-G		not specified	Uncertain significance (Dec 17, 2021)
14-52011047-C-T		not specified	Uncertain significance (Apr 12, 2024)
14-52011568-G-A		not specified	Uncertain significance (Feb 05, 2024)
14-52011589-T-G		not specified	Uncertain significance (Feb 22, 2023)
14-52011596-C-T		not specified	Likely benign (Oct 17, 2023)
14-52011599-C-T		not specified	Uncertain significance (May 23, 2023)
14-52011601-C-T		not specified	Uncertain significance (Apr 07, 2022)
14-52011649-C-T		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NID2	protein_coding	protein_coding	ENST00000216286	22	64192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.11e-9	1.00	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.250	826	806	1.02	0.0000448	8892
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000784	0.000775
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000328	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000250	0.000246
Middle Eastern	0.000328	0.000326
South Asian	0.000273	0.000261
Other	0.000491	0.000489

dbNSFP

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.
• Pathway: Laminin interactions;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.207

Intolerance Scores

• loftool: 0.113
• rvis_EVS: 3.6
• rvis_percentile_EVS: 99.53

Haploinsufficiency Scores

• pHI: 0.751
• hipred: Y
• hipred_score: 0.563
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.577

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nid2
• Phenotype: skeleton phenotype; cellular phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;cell-matrix adhesion;extracellular matrix organization;basement membrane organization
• Cellular component: extracellular region;basement membrane;plasma membrane;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent;calcium ion binding;protein binding;collagen binding