FAM47E-STBD1

protein-coding

FAM47E-STBD1 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring FAM47E (family with sequence similarity 47, member E) and STBD1 (starch binding domain 1) genes on chromosome 4. The read-through transcript encodes a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to frameshifts relative to the downstream gene. [provided by RefSeq, Jul 2011]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:18B:4

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr4:76,251,721-76,311,129

External References & Databases

Ensembl (ENSG00000272414)

NCBI Gene (100631383)

HGNC:44667

GenCC

ClinVar (FAM47E-STBD1)

Transcript & Mutation Effects

hg38 • Region Span ~59.4 kb

Loading mutation effect viewer...

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-STBD1 variants in ClinVar

1 Conditions Cataloged

Inborn genetic diseasesTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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			18 clinvar	4 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	4	0	22

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001242939.2	RefSeq	NP_001229868.1	7	Standard
ENST00000509377.1	Ensembl	ENSP00000425528.2	2	Standard
ENST00000514140.1	Ensembl	ENSP00000423044.2	5	Standard
ENST00000514365.5	Ensembl	ENSP00000424458.1	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000515604
Coding exons: 7
Length: 59409
Individuals with no LoFs: 105423
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 105424
p: 0.00000474

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.75	113	179	0.631	0.00000962	2284
Missense (PolyPhen)		20	36.128	0.55358		525
Synonymous	0.769	66	74.4	0.887	0.00000440	661
Loss of Function	1.93	6	13.7	0.438	5.75e-7	206

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)	0.0000099	0.0000099	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N

Gene Damage Prediction

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