FAM9A

protein-coding

family with sequence similarity 9 member A

Gene summary

This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein may be a nuclear protein that is localized to the nucleolus, and has some similarity to a synaptonemal complex protein. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Aug 2011]

MANE transcript

NM_174951.3

Inheritance

—

ClinVar variants

U:46B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.43

Max pathogenic AF

—

Genomic locus

chrX:8,790,795-8,801,383

External References & Databases

Ensembl (ENSG00000183304)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 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 FAM9A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174951.3. 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					1 clinvar	1
missense			46 clinvar	5 clinvar		51
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	6	1	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174951.3	RefSeq	NP_777611.1	8	MANE Select
ENST00000381003.7	Ensembl	ENSP00000370391.3	8	MANE Select
NM_001171186.1	RefSeq	NP_001164657.1	8	Standard
ENST00000543214.1	Ensembl	ENSP00000440163.1	8	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
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000543214
Coding exons: 8
Length: 10589
Individuals with no LoFs: 125730
Homozygous LoFs: 12
Heterozygous LoFs: 6
Defined: 125748
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.752	145	122	1.19	0.00000982	2182
Missense (PolyPhen)		25	19.951	1.2531		242
Synonymous	-0.288	46	43.6	1.06	0.00000375	577
Loss of Function	-1.29	15	10.5	1.43	6.63e-7	243

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000037	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00024	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000076	0.000053	rare
South Asian	0.00043	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.276
RVIS EVS: 0.28
RVIS percentile EVS: 71.27

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