FAM89A

family with sequence similarity 89 member A, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:231018958-231040254

Previous symbols: [ "C1orf153" ]

Links

ENSG00000182118 ∙ NCBI:375061 ∙ ∙ HGNC:25057 ∙ Uniprot:Q96GI7 ∙ 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 FAM89A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM89A 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in FAM89A

This is a list of pathogenic ClinVar variants found in the FAM89A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-231019910-G-T		not specified	Uncertain significance (Dec 03, 2021)
1-231019939-T-G		not specified	Uncertain significance (Nov 15, 2024)
1-231019940-C-A		not specified	Uncertain significance (Nov 15, 2024)
1-231020014-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-231020038-G-C		not specified	Uncertain significance (Apr 06, 2022)
1-231020051-C-T		not specified	Uncertain significance (Jan 19, 2024)
1-231020066-T-A		not specified	Uncertain significance (Jun 25, 2024)
1-231020116-C-T		not specified	Uncertain significance (Nov 20, 2024)
1-231039965-G-C		not specified	Uncertain significance (Feb 13, 2024)
1-231039976-A-G		not specified	Likely benign (Nov 08, 2024)
1-231039982-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-231039989-G-A		not specified	Uncertain significance (Nov 25, 2024)
1-231040009-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-231040091-C-T		not specified	Uncertain significance (Nov 27, 2023)
1-231040119-C-G		not specified	Uncertain significance (May 01, 2024)
1-231040123-C-T		not specified	Uncertain significance (May 17, 2023)
1-231040124-T-C		not specified	Uncertain significance (Nov 01, 2022)
1-231040145-C-A		not specified	Uncertain significance (Sep 15, 2021)
1-231040151-C-T		not specified	Uncertain significance (May 16, 2024)
1-231040166-C-G		not specified	Uncertain significance (Nov 07, 2024)
1-231040168-G-A		not specified	Uncertain significance (Oct 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM89A	protein_coding	protein_coding	ENST00000366654	2	21289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.257	0.649	125683	0	6	125689	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.241	66	71.7	0.920	0.00000398	1137
Missense in Polyphen		22	30.221	0.72797		443
Synonymous	0.355	32	34.7	0.923	0.00000221	409
Loss of Function	1.23	1	3.48	0.287	1.49e-7	50

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)	0.0000536	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.231
• ghis: 0.445

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

Mouse Genome Informatics

• Gene name: Fam89a