NID1

Chr 1

nidogen 1

Also known as: NID

NCBI Gene: 4811 ENSG00000116962 UniProt: P14543 OMIM: 131390

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.

GeneReviews OMIM 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]

GeneReviews OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.65

LOEUF

—

Mechanism

📖

GeneReview available — NID1

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

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

Background carrier burden — how many people carry a rare variant somewhere in NID1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 28

1,624 rare PASS variants

Rare truncating (LoF)

1 in 1,300

142 rare PASS variants

Rare synonymous (reference)

1 in 45

710 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NID1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 38	1 in 1,100
South Asian	~43k	1 in 26	1 in 1,300
Remaining (unassigned)	~30k	1 in 25	1 in 3,000
European (Finnish)	~27k	1 in 71	1 in 2,400
Admixed American	~22k	1 in 25	1 in 1,500
African / African American	~21k	1 in 27	1 in 1,100
East Asian	~20k	1 in 32	1 in 1,100
Ashkenazi Jewish	~13k	1 in 110	none seen
Middle Eastern	~2,884	1 in 24	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 20 coding exons well covered in gnomAD exomes and genomes.? see exons ↓