FAM133A

family with sequence similarity 133 member A

Basic information

Region (hg38): X:93674012-93712274

Links

ENSG00000179083 ∙ NCBI:286499 ∙ ∙ HGNC:26748 ∙ Uniprot:Q8N9E0 ∙ 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 FAM133A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM133A 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	2		9
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	2	0

Variants in FAM133A

This is a list of pathogenic ClinVar variants found in the FAM133A 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-93709430-G-A		not specified	Uncertain significance (Feb 27, 2024)
X-93709486-A-G		not specified	Uncertain significance (Feb 06, 2024)
X-93709726-C-T			Likely benign (Dec 01, 2022)
X-93709788-G-C			Likely benign (Nov 15, 2018)
X-93709964-A-G		not specified	Uncertain significance (Nov 07, 2023)
X-93710003-C-T		not specified	Uncertain significance (Jun 22, 2023)
X-93710051-G-A		not specified	Uncertain significance (Feb 14, 2023)
X-93710065-G-C		not specified	Uncertain significance (Jul 19, 2022)
X-93710081-A-G		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM133A	protein_coding	protein_coding	ENST00000538690	1	38262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.396	0.567	119206	2	4	119212	0.0000252

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0717	64	65.6	0.975	0.00000464	1597
Missense in Polyphen		8	17.284	0.46286		414
Synonymous	-0.190	25	23.8	1.05	0.00000153	419
Loss of Function	1.66	1	5.00	0.200	3.68e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000851	0.0000637
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000817	0.0000573
Finnish	0.00	0.00
European (Non-Finnish)	0.0000408	0.0000273
Middle Eastern	0.0000817	0.0000573
South Asian	0.0000650	0.0000378
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0926

Intolerance Scores

• loftool: 0.446
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.12

Haploinsufficiency Scores

• pHI: 0.298
• hipred: N
• hipred_score: 0.173
• ghis: 0.419

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	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Molecular function: protein binding