NID1

Chr 1

nidogen 1

Also known as: NID

NCBI Gene: 4811 ENSG00000116962 UniProt: P14543

The protein is a sulfated glycoprotein that binds to laminin, collagen IV, and perlecan in basement membranes throughout the body. Mutations cause autosomal recessive congenital muscular dystrophy with intellectual disability, structural brain abnormalities, and eye defects. This gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely incompatible with normal development.

ResearchSummary from RefSeq, UniProt

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]

ResearchGenerating clinical summary…

LOEUF 0.65

Clinical Summary— NID1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

2 unique Pathogenic / Likely Pathogenic· 200 VUS of 317 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.65LOEUF

pLI 0.000

Z-score 3.78

OE 0.48 (0.35–0.65)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.48Z-score

OE missense 0.95 (0.90–1.01)

743 obs / 780.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.48 (0.35–0.65)

0≤0.351.4

Missense OE?0.95 (0.90–1.01)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 29 / 60.8Missense obs/exp: 743 / 780.9Syn Z: -0.20

ClinVar Variant Classifications

317 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Pathogenic2

VUS200

Likely Benign18

Benign73

Conflicting2

Likely Pathogenic

200

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	1	1	0	0	2
VUS	4	195	1	0	200
Likely Benign	0	9	0	9	18
Benign	0	12	49	12	73
Conflicting	—				2
Total	5	217	50	21	295

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

View in ClinVar →

51 pathogenic / likely-pathogenic (of 64) ClinVar copy-number / structural variants overlap NID1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →