FAM53C

family with sequence similarity 53 member C

Basic information

Region (hg38): 5:138331935-138349729

Previous symbols: [ "C5orf6" ]

Links

ENSG00000120709 ∙ NCBI:51307 ∙ OMIM:609372 ∙ HGNC:1336 ∙ Uniprot:Q9NYF3 ∙ 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 FAM53C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM53C 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in FAM53C

This is a list of pathogenic ClinVar variants found in the FAM53C region.

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

Position	Type	Phenotype	Significance	ClinVar
5-138341354-G-A		not specified	Uncertain significance (Nov 21, 2024)
5-138341372-A-T		not specified	Uncertain significance (Mar 01, 2025)
5-138341397-G-A		not specified	Uncertain significance (Sep 26, 2024)
5-138341829-C-A		not specified	Uncertain significance (Jan 16, 2025)
5-138344869-T-C		not specified	Uncertain significance (Apr 25, 2022)
5-138344884-A-C		not specified	Uncertain significance (Jul 02, 2024)
5-138344917-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-138344932-A-G		not specified	Uncertain significance (Jan 31, 2023)
5-138344935-C-T		not specified	Uncertain significance (Oct 27, 2021)
5-138344936-G-A		not specified	Uncertain significance (Feb 21, 2024)
5-138344943-C-CT		Autism	Uncertain significance (-)
5-138344948-C-A		not specified	Uncertain significance (Feb 28, 2023)
5-138344986-C-T		not specified	Uncertain significance (Jan 17, 2025)
5-138345043-C-T		not specified	Uncertain significance (Sep 27, 2022)
5-138345049-C-T		not specified	Uncertain significance (Oct 27, 2021)
5-138345073-C-T		not specified	Uncertain significance (Jul 06, 2021)
5-138345097-G-A		not specified	Uncertain significance (Mar 03, 2025)
5-138345118-C-A		not specified	Uncertain significance (Dec 10, 2024)
5-138345131-G-A		not specified	Uncertain significance (Jan 07, 2025)
5-138345145-G-A		not specified	Uncertain significance (Mar 01, 2025)
5-138345178-C-G		not specified	Uncertain significance (Feb 17, 2025)
5-138345178-C-T			Uncertain significance (-)
5-138345183-G-T		not specified	Uncertain significance (Apr 23, 2024)
5-138345185-G-A		not specified	Uncertain significance (Jun 30, 2022)
5-138345254-A-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM53C	protein_coding	protein_coding	ENST00000239906	4	17793

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0676	0.930	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.669	212	241	0.879	0.0000162	2511
Missense in Polyphen		54	72.837	0.74138		650
Synonymous	-0.359	98	93.6	1.05	0.00000525	861
Loss of Function	2.64	5	16.6	0.301	0.00000103	155

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)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.408
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.661
• hipred: Y
• hipred_score: 0.533
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam53c

Gene ontology

• Molecular function: protein binding