SHROOM1

Chr 5

shroom family member 1

Also known as: APXL2

NCBI Gene: 134549ENSG00000164403UniProt: Q2M3G4

SHROOM family members play diverse roles in the development of the nervous system and other tissues (Hagens et al., 2006 [PubMed 16615870]).[supplied by OMIM, Mar 2008]

0
Active trials
15
Pathogenic / LP
154
ClinVar variants
1
Pubs (1 yr)
0.9
Missense Z
0.54
LOEUF
Clinical Summary— SHROOM1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.29) despite low pLI — interpret in context.
📋
ClinVar Variants
15 Pathogenic / Likely Pathogenic· 128 VUS of 154 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.54LOEUF
pLI 0.046
Z-score 3.25
OE 0.29 (0.16–0.54)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.92Z-score
OE missense 0.88 (0.81–0.95)
397 obs / 452.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.29 (0.16–0.54)
0≤0.351.4
Missense OE0.88 (0.81–0.95)
0≤0.61.4
Synonymous OE0.82
0≤1.21.6
LoF obs/exp: 7 / 24.3Missense obs/exp: 397 / 452.2Syn Z: 1.99

ClinVar Variant Classifications

154 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic1
VUS128
Likely Benign10
Benign1
14
Pathogenic
1
Likely Pathogenic
128
VUS
10
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
14
0
14
Likely Pathogenic
0
0
1
0
1
VUS
0
126
2
0
128
Likely Benign
0
7
1
2
10
Benign
0
0
0
1
1
Total0133183154

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

View in ClinVar →

SHROOM1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients