FAM153A

family with sequence similarity 153 member A

Basic information

Region (hg38): 5:177707981-177784435

Links

ENSG00000170074 ∙ NCBI:285596 ∙ ∙ HGNC:29940 ∙ Uniprot:Q9UHL3 ∙ 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 FAM153A gene.

• not_specified (31 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM153A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001413826.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			31			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM153A	protein_coding	protein_coding	ENST00000440605	19	75418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000670	0.728	125719	3	25	125747	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.498	97	112	0.868	0.00000592	1998
Missense in Polyphen		16	24.426	0.65504		538
Synonymous	-0.191	44	42.4	1.04	0.00000239	556
Loss of Function	1.12	10	14.6	0.683	6.62e-7	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000972	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000801	0.000601
European (Non-Finnish)	0.000113	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000450	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00414

Gene Damage Prediction

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