FAM90A1

protein-coding

family with sequence similarity 90 member A1

Gene summary

FAM90A1 belongs to subfamily I of the primate-specific FAM90A gene family, which originated from multiple duplications and rearrangements (Bosch et al., 2007 [PubMed 17684299]).[supplied by OMIM, Oct 2009]

MANE transcript

NM_018088.3

Inheritance

—

ClinVar variants

U:95B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.24

Max pathogenic AF

—

Genomic locus

chr12:8,221,260-8,227,618

External References & Databases

Ensembl (ENSG00000171847)

Transcript & Mutation Effects

hg38 • Region Span ~6.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM90A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 97

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018088.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			95 clinvar	6 clinvar		101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	95	8	0	103

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018088.3	RefSeq	NP_060558.3	4	MANE Select
ENST00000538603.6	Ensembl	ENSP00000445418.1	4	MANE Select
NM_001319982.2	RefSeq	NP_001306911.1	4	Standard
ENST00000307435.10	Ensembl	ENSP00000307798.6	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000538603
Coding exons: 4
Length: 6359
Individuals with no LoFs: 121766
Homozygous LoFs: 42
Heterozygous LoFs: 3763
Defined: 125571
p: 0.0153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.43	328	263	1.25	0.0000171	2916
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.0074	0.0073	notable
Ashkenazi Jewish	0.042	0.042	notable
East Asian	0.000056	0.000054	rare
Finnish	0.031	0.026	notable
European (Non-Finnish)	0.014	0.013	notable
South Asian	0.033	0.032	notable
Other	0.018	0.017	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0723

Intolerance Scores

LoFtool: 0.897
RVIS EVS: 1.98
RVIS percentile EVS: 97.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.442

Gene Damage Prediction

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