FAM9C

protein-coding

family with sequence similarity 9 member C

Gene summary

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]

MANE transcript

NM_174901.6

Inheritance

—

ClinVar variants

U:20B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.57

Max pathogenic AF

—

Genomic locus

chrX:13,035,617-13,044,682

External References & Databases

Ensembl (ENSG00000187268)

Transcript & Mutation Effects

hg38 • Region Span ~9.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM9C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174901.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			19 clinvar	1 clinvar		20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	20	1	0	21

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174901.6	RefSeq	NP_777561.1	6	MANE Select
ENST00000380625.8	Ensembl	ENSP00000369999.3	6	MANE Select
ENST00000333995.7	Ensembl	ENSP00000334430.3	6	Standard
ENST00000333995.8	Ensembl	ENSP00000334430.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
spermatid development
meiotic cell cycle

Molecular Function

protein binding

Cellular Component

synaptonemal complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333995
Coding exons: 6
Length: 9065
Individuals with no LoFs: 121764
Homozygous LoFs: 32
Heterozygous LoFs: 19
Defined: 121815
p: 0.000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.159	51	54.3	0.939	0.00000386	1109
Missense (PolyPhen)		6	7.9187	0.7577		203
Synonymous	-0.553	20	17.1	1.17	0.00000122	263
Loss of Function	-1.19	8	5.10	1.57	3.20e-7	114

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000077	0.000054	rare
South Asian	0.0029	0.0015	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.767
RVIS EVS: -0.21
RVIS percentile EVS: 38.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium