FAM90A1

family with sequence similarity 90 member A1

Basic information

Region (hg38): 12:8221260-8227618

Links

ENSG00000171847 ∙ NCBI:55138 ∙ OMIM:613041 ∙ HGNC:25526 ∙ Uniprot:Q86YD7 ∙ 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 FAM90A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM90A1 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				2		2
missense			43	5	3	51
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	7	4

Variants in FAM90A1

This is a list of pathogenic ClinVar variants found in the FAM90A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-8221826-T-C		not specified	Uncertain significance (Mar 06, 2025)
12-8221860-G-A		not specified	Likely benign (Mar 04, 2024)
12-8221910-C-G		not specified	Likely benign (Sep 01, 2021)
12-8221917-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-8221952-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-8221952-G-C		not specified	Uncertain significance (Jul 19, 2023)
12-8221958-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-8221980-A-T		not specified	Uncertain significance (Feb 10, 2022)
12-8221993-C-G			Likely benign (Oct 01, 2022)
12-8222010-G-A		not specified	Uncertain significance (Jan 24, 2025)
12-8222013-C-T		not specified	Uncertain significance (Oct 29, 2024)
12-8222019-C-G		not specified	Uncertain significance (Sep 13, 2023)
12-8222050-G-A			Likely benign (Mar 01, 2023)
12-8222074-G-T		not specified	Uncertain significance (Feb 22, 2025)
12-8222085-T-C		not specified	Uncertain significance (Jun 17, 2024)
12-8222090-C-T		not specified	Uncertain significance (Jan 08, 2025)
12-8222093-G-A		not specified	Uncertain significance (Nov 20, 2024)
12-8222112-A-G		not specified	Uncertain significance (Jul 06, 2021)
12-8222114-G-C		not specified	Uncertain significance (Aug 02, 2021)
12-8222124-G-A		not specified	Uncertain significance (Nov 25, 2024)
12-8222142-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-8222150-A-G		not specified	Uncertain significance (Apr 12, 2024)
12-8222185-C-CACG			Benign (Aug 09, 2017)
12-8222208-C-T		not specified	Uncertain significance (May 30, 2023)
12-8222237-G-A		not specified	Uncertain significance (Jan 25, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM90A1	protein_coding	protein_coding	ENST00000538603	4	6359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000156	0.133	121766	42	3763	125571	0.0153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.43	328	263	1.25	0.0000171	2916
Missense in Polyphen		46	42.536	1.0814		558
Synonymous	-3.47	159	112	1.42	0.00000882	963
Loss of Function	-0.564	8	6.45	1.24	2.75e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00894	0.00884
Ashkenazi Jewish	0.0424	0.0420
East Asian	0.0000557	0.0000544
Finnish	0.0313	0.0260
European (Non-Finnish)	0.0137	0.0133
Middle Eastern	0.0000557	0.0000544
South Asian	0.0327	0.0318
Other	0.0178	0.0168

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0723

Intolerance Scores

• loftool: 0.897
• rvis_EVS: 1.98
• rvis_percentile_EVS: 97.62

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.139
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.442

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Molecular function: protein binding