SVOPL

protein-coding

SVOP like, the group of Solute carrier family 22

Gene summary

The protein encoded by this gene is thought to be a member of solute carrier family 22, which includes transmembrane proteins that transport toxins and drugs from the body. This gene is a paralog of the SVOP gene that encodes synaptic vesicle 2-related protein. [provided by RefSeq, Sep 2016]

MANE transcript

NM_001139456.2

Inheritance

—

ClinVar variants

U:110B:11

Top phenotype

Non-immune hydrops fetalis

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr7:138,594,285-138,701,362

External References & Databases

Ensembl (ENSG00000157703)

Transcript & Mutation Effects

hg38 • Region Span ~107.1 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 SVOPL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 6

Non-immune hydrops fetalisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001139456.2. 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	1 clinvar	3
missense			109 clinvar	5 clinvar	2 clinvar	116
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	110	8	3	121

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001139456.2	RefSeq	NP_001132928.1	15	MANE Select
ENST00000674285.1	Ensembl	ENSP00000501457.1	15	MANE Select
NM_001331192.1	RefSeq	NP_001318121.1	12	Standard
NM_174959.3	RefSeq	NP_777619.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transmembrane transport

Molecular Function

transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419765
Coding exons: 15
Length: 107068
Individuals with no LoFs: 125027
Homozygous LoFs: 1
Heterozygous LoFs: 720
Defined: 125748
p: 0.00287

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.334	323	307	1.05	0.0000188	3147
Missense (PolyPhen)		105	101.74	1.032		1014
Synonymous	-0.957	136	123	1.11	0.00000780	1033
Loss of Function	1.63	17	26.0	0.655	0.00000110	319

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0011	notable
Latino/Admixed American	0.0033	0.0033	notable
Ashkenazi Jewish	0.0037	0.0037	notable
East Asian	0.00049	0.00049	rare
Finnish	0.00055	0.00055	rare
European (Non-Finnish)	0.0043	0.0043	notable
South Asian	0.00069	0.00065	rare
Other	0.0041	0.0041	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.946
RVIS EVS: -0.06
RVIS percentile EVS: 48.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0236

Gene Damage Prediction

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