FAM89B

Chr 11

family with sequence similarity 89 member B

Also known as: LRAP25, MTVR, MTVR1

NCBI Gene: 23625ENSG00000176973UniProt: Q8N5H3

Predicted to enable transcription corepressor binding activity. Predicted to be involved in establishment of cell polarity; negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway; and positive regulation of cell migration. Predicted to be located in cell projection. Predicted to be active in cytoplasm and lamellipodium. [provided by Alliance of Genome Resources, Jul 2025]

47
ClinVar variants
9
Pathogenic / LP
0.05
pLI score
0
Active trials
Clinical Summary— FAM89B
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.05) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
9 Pathogenic / Likely Pathogenic· 32 VUS of 47 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.
1.65LOEUF
pLI 0.052
Z-score 0.70
OE 0.59 (0.24–1.65)
Tolerant

Highly tolerant — LoF variants common in population

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.
1.05Z-score
OE missense 0.61 (0.46–0.81)
35 obs / 57.4 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.0.59 (0.24–1.65)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.61 (0.46–0.81)
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.0.96
0≤1.21.6
LoF obs/exp: 2 / 3.4Missense obs/exp: 35 / 57.4Syn Z: 0.19

ClinVar Variant Classifications

47 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7
Likely Pathogenic2
VUS32
Likely Benign6
7
Pathogenic
2
Likely Pathogenic
32
VUS
6
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
7
0
7
Likely Pathogenic
0
0
2
0
2
VUS
0
27
5
0
32
Likely Benign
0
6
0
0
6
Benign
0
0
0
0
0
Total03314047

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

View in ClinVar →

Protein Context — Lollipop Plot

FAM89B · 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
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Identifying diagnostic biomarkers for glaucoma based on transcriptome combined with Mendelian randomization.
Lin X et al.·Sci Rep
2025
Notch signaling in mammary gland tumorigenesis.
Callahan R et al.·J Mammary Gland Biol Neoplasia
2001Review
Integrative genomics reveals mechanisms of copy number alterations responsible for transcriptional deregulation in colorectal cancer.
Camps J et al.·Genes Chromosomes Cancer
2009Functional
Changes in attitude, changes in latitude: nuclear receptors remodeling chromatin to regulate transcription.
Chen J et al.·Mol Endocrinol
2006Review
Adaptor protein LRAP25 mediates myotonic dystrophy kinase-related Cdc42-binding kinase (MRCK) regulation of LIMK1 protein in lamellipodial F-actin dynamics.
Lee ICJ et al.·J Biol Chem
2014
Epithelial mesenchymal transition is a characteristic of hyperplasias and tumors in mammary gland from MMTV-Cripto-1 transgenic mice.
Strizzi L et al.·J Cell Physiol
2004
Stromal cell expression of caveolin-1 predicts outcome in breast cancer.
Sloan EK et al.·Am J Pathol
2009
The role of the cyclin D1-dependent kinases in ErbB2-mediated breast cancer.
Yang C et al.·Am J Pathol
2004
A novel membrane protein is a mouse mammary tumor virus receptor.
Golovkina TV et al.·J Virol
1998Functional
Failure of steroid regulation of the MMTV promoter in a small cell lung cancer cell line is caused by a DNA sequence flanking the glucocorticoid response element.
Huynh TT et al.·J Endocrinol
2002
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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