FAM53B

family with sequence similarity 53 member B

Basic information

Region (hg38): 10:124619292-124744378

Previous symbols: [ "KIAA0140" ]

Links

ENSG00000189319 ∙ NCBI:9679 ∙ OMIM:617289 ∙ HGNC:28968 ∙ Uniprot:Q14153 ∙ 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 FAM53B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM53B 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in FAM53B

This is a list of pathogenic ClinVar variants found in the FAM53B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-124623279-T-A		not specified	Uncertain significance (Oct 06, 2022)
10-124623307-C-A		not specified	Uncertain significance (Jan 19, 2022)
10-124623312-C-T		not specified	Uncertain significance (Sep 28, 2022)
10-124623319-G-A		not specified	Uncertain significance (Dec 19, 2023)
10-124623324-G-C		not specified	Uncertain significance (May 09, 2023)
10-124623415-G-C		not specified	Uncertain significance (May 12, 2024)
10-124623499-C-T		not specified	Uncertain significance (Apr 25, 2023)
10-124623537-G-A		not specified	Uncertain significance (Mar 15, 2024)
10-124623538-G-C		not specified	Uncertain significance (Aug 26, 2022)
10-124623601-A-G		not specified	Uncertain significance (Feb 17, 2024)
10-124681738-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-124681743-G-A		not specified	Uncertain significance (Dec 21, 2022)
10-124681804-A-C		not specified	Uncertain significance (Apr 08, 2024)
10-124681807-A-C		not specified	Uncertain significance (Dec 16, 2021)
10-124681841-G-C		not specified	Uncertain significance (Oct 12, 2021)
10-124681861-C-T		not specified	Likely benign (Nov 17, 2022)
10-124681902-C-T		not specified	Uncertain significance (Apr 15, 2024)
10-124681914-C-A		not specified	Uncertain significance (Mar 20, 2024)
10-124681947-C-A		not specified	Uncertain significance (Dec 01, 2022)
10-124682053-G-A		not specified	Uncertain significance (Nov 14, 2023)
10-124682067-C-A		not specified	Uncertain significance (Jun 06, 2023)
10-124682079-C-T		not specified	Uncertain significance (Jan 31, 2022)
10-124682104-C-T		not specified	Uncertain significance (Feb 28, 2023)
10-124682144-C-T		not specified	Uncertain significance (Jun 02, 2024)
10-124682169-C-A		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM53B	protein_coding	protein_coding	ENST00000337318	4	124978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.855	0.145	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	215	271	0.793	0.0000176	2724
Missense in Polyphen		59	90.05	0.65519		870
Synonymous	-1.09	129	114	1.13	0.00000806	868
Loss of Function	3.13	2	15.1	0.132	8.10e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulator of Wnt signaling pathway by regulating beta-catenin (CTNNB1) nuclear localization. {ECO:0000269|PubMed:25183871}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.193
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.259
• hipred: N
• hipred_score: 0.410
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.179

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam53b
• Phenotype: hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: fam53b
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased branchiness

Gene ontology

• Biological process: Wnt signaling pathway;regulation of canonical Wnt signaling pathway;positive regulation of canonical Wnt signaling pathway
• Cellular component: nucleus