FAM53A

family with sequence similarity 53 member A

Basic information

Region (hg38): 4:1617914-1684313

Links

ENSG00000174137 ∙ NCBI:152877 ∙ OMIM:617229 ∙ HGNC:31860 ∙ Uniprot:Q6NSI3 ∙ 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 FAM53A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM53A 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	4	5
missense			34	4	6	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	5	10

Variants in FAM53A

This is a list of pathogenic ClinVar variants found in the FAM53A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-1641319-C-T		not specified	Uncertain significance (Feb 22, 2023)
4-1641331-G-A		not specified	Uncertain significance (Feb 27, 2024)
4-1641346-C-T		not specified	Likely benign (Jan 07, 2022)
4-1641358-C-T		not specified	Uncertain significance (Jun 22, 2023)
4-1641388-T-C		not specified	Uncertain significance (Dec 13, 2022)
4-1641396-C-T		not specified	Uncertain significance (Sep 27, 2022)
4-1641397-G-A		not specified	Uncertain significance (Dec 12, 2023)
4-1641417-G-A		not specified	Uncertain significance (Jun 03, 2024)
4-1641439-T-G		not specified	Uncertain significance (Dec 11, 2023)
4-1641463-G-A		not specified	Uncertain significance (Jul 20, 2022)
4-1641465-C-A		not specified	Uncertain significance (Dec 30, 2023)
4-1641486-A-G		not specified	Likely benign (Jan 19, 2024)
4-1641504-C-A		not specified	Uncertain significance (May 09, 2024)
4-1641544-G-A		not specified	Uncertain significance (Nov 17, 2022)
4-1641601-T-G		not specified	Uncertain significance (Jun 09, 2022)
4-1655010-G-A		not specified	Uncertain significance (Jan 19, 2022)
4-1655021-G-A		not specified	Uncertain significance (Apr 12, 2022)
4-1655033-C-T			Benign (Jun 05, 2018)
4-1655034-G-A		not specified	Uncertain significance (May 27, 2022)
4-1655046-G-A		not specified	Uncertain significance (Feb 28, 2023)
4-1655049-G-C			Benign (Apr 10, 2018)
4-1655054-C-T		not specified	Likely benign (Dec 13, 2022)
4-1655070-C-A		not specified	Uncertain significance (Nov 09, 2021)
4-1655095-C-G			Benign (Apr 10, 2018)
4-1655097-G-A			Benign (Jun 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM53A	protein_coding	protein_coding	ENST00000308132	4	66388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00357	0.853	125708	0	25	125733	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.445	244	225	1.08	0.0000156	2468
Missense in Polyphen		63	65.139	0.96717		776
Synonymous	-0.582	107	99.6	1.07	0.00000741	842
Loss of Function	1.22	5	8.96	0.558	4.49e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000786	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.000529	0.000523
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in neural development; the dorsomedial roof of the third ventricle. {ECO:0000250|UniProtKB:Q5ZKN5}.

Haploinsufficiency Scores

• pHI: 0.0865
• hipred: N
• hipred_score: 0.187
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam53a

Gene ontology

• Cellular component: nucleus