FAM47E

protein-coding

family with sequence similarity 47 member E

Gene summary

Enables enzyme activator activity. Involved in protein localization to chromatin and transcription initiation-coupled chromatin remodeling. Located in chromatin; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001136570.3

Inheritance

—

ClinVar variants

U:52B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr4:76,214,040-76,283,783

External References & Databases

Ensembl (ENSG00000189157)

NCBI Gene (100129583)

Transcript & Mutation Effects

hg38 • Region Span ~69.7 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 FAM47E variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 57

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001136570.3. 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						0
missense			51 clinvar	6 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	52	6	0	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001136570.3	RefSeq	NP_001130042.1	8	MANE Select
ENST00000424749.7	Ensembl	ENSP00000409423.2	8	MANE Select
NM_001242936.1	RefSeq	NP_001229865.1	7	Standard
ENST00000502320.2	Ensembl	ENSP00000490159.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000424749
Coding exons: 8
Length: 69741
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.84	127	200	0.634	0.0000109	2551
Missense (PolyPhen)		23	42.88	0.53638		643
Synonymous	1.20	69	82.9	0.832	0.00000494	743
Loss of Function	1.99	7	15.4	0.453	6.49e-7	233

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.48
RVIS percentile EVS: 95.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.106

Gene Damage Prediction

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