ARHGAP19-SLIT1

ncRNA

ARHGAP19-SLIT1 readthrough (NMD candidate)

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring Rho GTPase activating protein 19 (ARHGAP19) and slit homolog 1 (SLIT1) genes on chromosome 10. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

MANE transcript

N/A

Inheritance

—

ClinVar variants

—

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr10:97,153,045-97,292,637

External References & Databases

Ensembl (ENSG00000269891)

NCBI Gene (100533184)

HGNC:48348

GenCC

ClinVar (ARHGAP19-SLIT1)

Transcript & Mutation Effects

hg38 • Region Span ~139.6 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 ARHGAP19-SLIT1 variants in ClinVar

2 Conditions Cataloged

Inborn genetic diseasesTotal: 27

not providedTotal: 2

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
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 1 of 1 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
ENST00000479633.2	Ensembl	ENSP00000473567.1	13	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000453547
Coding exons: 13
Length: 294619
Individuals with no LoFs: 125644
Homozygous LoFs: 1
Heterozygous LoFs: 103
Defined: 125748
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.334	272	288	0.945	0.0000155	3389
Missense (PolyPhen)		73	89.519	0.81547		1065
Synonymous	1.33	89	107	0.836	0.00000567	990
Loss of Function	1.51	22	31.1	0.708	0.00000181	352

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00071	0.00071	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.00092	0.00088	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Gene Damage Prediction

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