FAM9C

Chr X

family with sequence similarity 9 member C

Also known as: TEX39C

NCBI Gene: 171484 ENSG00000187268 UniProt: Q8IZT9 OMIM: 300479

The encoded protein is a nuclear-localized protein with similarity to synaptonemal complex proteins, which are involved in chromosome pairing during meiosis. This gene shows very low constraint against loss-of-function variants, and no definitive disease associations have been established for FAM9C mutations. The gene is located on the X chromosome and arose through gene duplication events.

OMIM ResearchSummary from RefSeq

This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein may be localized to the nucleus as the protein contains several nuclear localization signals, and has similarity to a synaptonemal complex protein. [provided by RefSeq, Aug 2011]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.94

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.94LOEUF

pLI 0.000

Z-score -1.19

OE 1.57 (0.85–1.94)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.16Z-score

OE missense 0.94 (0.75–1.19)

51 obs / 54.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.57 (0.85–1.94)

0≤0.351.4

Missense OE?0.94 (0.75–1.19)

0≤0.61.4

Synonymous OE?1.17

0≤1.21.6

LoF obs/exp: 8 / 5.1Missense obs/exp: 51 / 54.3Syn Z: -0.55

Background carrier burden — how many people carry a rare variant somewhere in FAM9C?

gnomAD v4 · ~732k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 270

162 rare PASS variants

Rare truncating (LoF)

1 in 1,700

36 rare PASS variants

Rare synonymous (reference)

1 in 1,500

66 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for FAM9C. 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)	~561k	1 in 600	1 in 2,700
South Asian	~36k	1 in 210	1 in 1,100
Remaining (unassigned)	~31k	1 in 160	1 in 910
European (Finnish)	~27k	1 in 5,400	none seen
Admixed American	~23k	1 in 250	1 in 1,100
African / African American	~21k	1 in 300	1 in 3,100
East Asian	~20k	1 in 510	≈ 1 in 10,000
Ashkenazi Jewish	~13k	≈ 1 in 11,000	none seen
Middle Eastern	~2,758	≈ 1 in 890	≈ 1 in 2,700

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 6 coding exons well covered in gnomAD exomes and genomes.? see exons ↓