FAM9B

Chr X

family with sequence similarity 9 member B

Also known as: TEX39B

NCBI Gene: 171483ENSG00000177138UniProt: Q8IZU0OMIM: 300478

The FAM9B protein may function in meiosis and contains nuclear localization signals with similarity to synaptonemal complex proteins. This gene is highly constrained against loss-of-function variants (pLI 0.00003) but currently lacks well-established disease associations in clinical databases. FAM9B is located on the X chromosome as part of a duplicated gene family.

OMIMResearchSummary from RefSeq, UniProt
LOEUF 1.69
Clinical Summary— FAM9B
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
87 unique Pathogenic / Likely Pathogenic· 32 VUS of 129 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.69LOEUF
pLI 0.000
Z-score 0.13
OE 0.95 (0.54–1.69)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.63Z-score
OE missense 1.22 (1.02–1.47)
81 obs / 66.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.95 (0.54–1.69)
0≤0.351.4
Missense OE1.22 (1.02–1.47)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 7 / 7.4Missense obs/exp: 81 / 66.5Syn Z: 0.01

ClinVar Variant Classifications

129 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic85
Likely Pathogenic2
VUS32
Likely Benign4
Benign2
85
Pathogenic
2
Likely Pathogenic
32
VUS
4
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
85
0
85
Likely Pathogenic
0
0
2
0
2
VUS
0
29
3
0
32
Likely Benign
0
1
2
1
4
Benign
0
1
1
0
2
Total031931125

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

View in ClinVar →

Protein Context — Lollipop Plot

FAM9B · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
X-chromosome and kidney function: evidence from a multi-trait genetic analysis of 908,697 individuals reveals sex-specific and sex-differential findings in genes regulated by androgen response elements
Scholz M et al.·Nat Commun
2024
The role of testosterone, the androgen receptor, and hypothalamic-pituitary-gonadal axis in depression in ageing Men
Hauger RL et al.·Rev Endocr Metab Disord
2022
A Population-Based Human In Vitro Approach to Quantify Inter-Individual Variability in Responses to Chemical Mixtures
Ford LC et al.·Toxics
2022
Comprehensive Human Red Blood Cell Membrane and Cytoplasmic Proteome Analyses
Zhang X et al.·Sci Data
2026
Mutation spectrum and frequency of copy number variations of the ANOS1 gene in patients with Kallmann syndrome or normosmic isolated hypogonadotropic hypogonadism
Hye Kim J et al.·Endocr Connect
2023Cohort
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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