FAM104B

family with sequence similarity 104 member B

Basic information

Region (hg38): X:55143101-55161310

Previous symbols: [ "CXorf44" ]

Links

ENSG00000182518 ∙ NCBI:90736 ∙ ∙ HGNC:25085 ∙ Uniprot:Q5XKR9 ∙ 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 FAM104B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM104B 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				1		1
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	1	0

Variants in FAM104B

This is a list of pathogenic ClinVar variants found in the FAM104B 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-55143826-C-T		not specified	Uncertain significance (Nov 21, 2023)
X-55146163-C-G		not specified	Uncertain significance (Oct 12, 2021)
X-55146177-A-G		not specified	Likely benign (Nov 25, 2024)
X-55146205-T-G			Likely benign (-)
X-55146214-G-A		not specified	Uncertain significance (Aug 02, 2021)
X-55146226-A-G		not specified	Uncertain significance (Sep 21, 2021)
X-55159157-G-A		not specified	Uncertain significance (May 14, 2024)
X-55159199-C-A		not specified	Uncertain significance (Dec 14, 2021)
X-55159228-C-T			Likely benign (Feb 01, 2025)
X-55160865-A-G			Likely benign (-)
X-55161143-G-C		not specified	Uncertain significance (Jan 31, 2024)
X-55161146-C-A		not specified	Uncertain significance (Jan 31, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM104B	protein_coding	protein_coding	ENST00000425133	3	18209

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0176	0.501	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.218	45	41.1	1.10	0.00000284	767
Missense in Polyphen		19	16.12	1.1786		312
Synonymous	0.469	12	14.3	0.842	9.12e-7	198
Loss of Function	-0.460	2	1.41	1.42	8.89e-8	28

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.67

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.112
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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