FAM199X

family with sequence similarity 199, X-linked

Basic information

Region (hg38): X:104166453-104195902

Previous symbols: [ "CXorf39" ]

Links

ENSG00000123575 ∙ NCBI:139231 ∙ ∙ HGNC:25195 ∙ Uniprot:Q6PEV8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM199X gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM199X gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in FAM199X

This is a list of pathogenic ClinVar variants found in the FAM199X region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-104175677-G-T		not specified	Uncertain significance (Jan 08, 2025)
X-104186130-G-T		not specified	Uncertain significance (Dec 09, 2024)
X-104186168-C-T		not specified	Uncertain significance (Dec 04, 2024)
X-104186169-G-A		not specified	Conflicting classifications of pathogenicity (Oct 28, 2024)
X-104188098-A-G		not specified	Uncertain significance (Feb 23, 2023)
X-104188155-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
X-104188157-A-G		not specified	Uncertain significance (Dec 11, 2024)
X-104188160-A-G		not specified	Uncertain significance (Mar 02, 2023)
X-104188271-T-A		not specified	Uncertain significance (Nov 11, 2024)
X-104189681-G-A		not specified	Uncertain significance (Sep 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM199X	protein_coding	protein_coding	ENST00000493442	6	29283

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.573	0.425	125727	3	0	125730	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	63	149	0.423	0.0000113	2588
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000386	0.0000386
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.181
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.268
• hipred: Y
• hipred_score: 0.662
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam199x

Gene ontology

• Molecular function: protein binding