FAM9B

protein-coding

family with sequence similarity 9 member B

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_205849.3

Inheritance

—

ClinVar variants

U:30B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chrX:9,024,232-9,295,682

External References & Databases

Ensembl (ENSG00000177138)

Transcript & Mutation Effects

hg38 • Region Span ~271.5 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 FAM9B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_205849.3. 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			29 clinvar	1 clinvar	1 clinvar	31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	30	2	1	33

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_205849.3	RefSeq	NP_995321.1	7	MANE Select
ENST00000327220.10	Ensembl	ENSP00000318716.5	7	MANE Select
ENST00000362066.7	Ensembl	ENSP00000354770.3	7	Standard
ENST00000428477.1	Ensembl	ENSP00000412606.1	7	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
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327220
Coding exons: 7
Length: 140408
Individuals with no LoFs: 125690
Homozygous LoFs: 2
Heterozygous LoFs: 22
Defined: 125714
p: 0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.630	81	66.5	1.22	0.00000521	1257
Missense (PolyPhen)		35	27.513	1.2721		511
Synonymous	0.0114	21	21.1	0.997	0.00000162	281
Loss of Function	0.133	7	7.39	0.947	4.65e-7	158

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0.00054	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000087	0.000062	rare
South Asian	0	0.0	absent
Other	0.00025	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.481
RVIS EVS: 0.04
RVIS percentile EVS: 56.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0588

Gene Damage Prediction

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