NID1

Chr 1

nidogen 1

Also known as: NID

NCBI Gene: 4811ENSG00000116962UniProt: P14543

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]

356
ClinVar variants
52
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NID1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
52 Pathogenic / Likely Pathogenic· 211 VUS of 356 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.65LOEUF
pLI 0.000
Z-score 3.78
OE 0.48 (0.35–0.65)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.48Z-score
OE missense 0.95 (0.90–1.01)
743 obs / 780.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.48 (0.35–0.65)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.95 (0.90–1.01)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.01
0≤1.21.6
LoF obs/exp: 29 / 60.8Missense obs/exp: 743 / 780.9Syn Z: -0.20

ClinVar Variant Classifications

356 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic48
Likely Pathogenic4
VUS211
Likely Benign18
Benign73
Conflicting2
48
Pathogenic
4
Likely Pathogenic
211
VUS
18
Likely Benign
73
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
48
0
48
Likely Pathogenic
1
1
2
0
4
VUS
2
194
15
0
211
Likely Benign
0
9
0
9
18
Benign
0
12
49
12
73
Conflicting
—2
Total321611421356

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NID1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
NIDOGEN 1; NID1
MIM #131390 · *
📖
GeneReview available — NID1
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families.
Alazami AM et al.·Cell Rep
2015
Human Cytomegalovirus Interactions with the Basement Membrane Protein Nidogen 1.
Kuan MI et al.·J Virol
2021
Transcriptional profiling unveils molecular subgroups of adaptive and maladaptive right ventricular remodeling in pulmonary hypertension.
Khassafi F et al.·Nat Cardiovasc Res
2023Functional
Nidogen-1, a Player in KMT2A-Rearranged Pediatric Acute Myeloid Leukemia.
Vanhooren J et al.·Int J Mol Sci
2025
ETV4 interacts with LOXL2 to induce epigenetic activation of NID1 during colorectal cancer progression.
Jiang T et al.·Int J Biol Sci
2025
NID1 variant associated with occipital cephaloceles in a family expressing a spectrum of phenotypes.
McNiven V et al.·Am J Med Genet A
2019Case report
NID1, a new regulator of EMT required for metastasis and chemoresistance of ovarian cancer cells.
Zhou Y et al.·Oncotarget
2017
Loss of the extracellular protease ADAMTS1 reveals an antitumorigenic program involving the action of NIDOGEN-1 on macrophage polarization.
Caracuel-Peramos R et al.·Oncoimmunology
2025
ECM Proteins Nidogen-1 and Decorin Restore Functionality of Human Islets of Langerhans upon Hypoxic Conditions.
Jeyagaran A et al.·Adv Healthc Mater
2025Functional
HCMV Infection Reduces Nidogen-1 Expression, Contributing to Impaired Neural Rosette Development in Brain Organoids.
Ijezie EC et al.·J Virol
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools