FAM199X

Gene

family with sequence similarity 199, X-linked

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

CXorf39

MANE transcript

NM_207318.4

Inheritance

—

ClinVar variants

U:72B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chrX:104,166,453-104,195,902

External References & Databases

Ensembl (ENSG00000123575)

Transcript & Mutation Effects

hg38 • Region Span ~29.4 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 FAM199X variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 17

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207318.4. 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			11 clinvar			11
missense			46 clinvar	2 clinvar		48
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			12 clinvar			12
Total	0	0	72	2	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207318.4	RefSeq	NP_997201.1	6	MANE Select
ENST00000493442.2	Ensembl	ENSP00000417581.1	6	MANE Select
ENST00000878950.1	Ensembl	ENSP00000549009.1	5	Standard
ENST00000878950.2	Ensembl	ENSP00000549009.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000493442
Coding exons: 6
Length: 29283
Individuals with no LoFs: 125727
Homozygous LoFs: 3
Heterozygous LoFs: 0
Defined: 125730
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.50	63	149	0.423	0.0000113	2588
Missense (PolyPhen)		21	68.956	0.30454		1143
Synonymous	0.989	43	52.1	0.826	0.00000365	726
Loss of Function	2.54	2	11.2	0.179	8.36e-7	191

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000039	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000024	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.181
RVIS EVS: 0.01
RVIS percentile EVS: 54.63

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	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Low	Medium