SLC17A9

protein-coding

solute carrier family 17 member 9, the group of Solute carrier family 17

Gene summary

This gene encodes a member of a family of transmembrane proteins that are involved in the transport of small molecules. The encoded protein participates in the vesicular uptake, storage, and secretion of adenoside triphosphate (ATP) and other nucleotides. A mutation in this gene was found in individuals with autosomal dominant disseminated superficial actinic porokeratosis-8. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

Previous symbols:

C20orf59

MANE transcript

NM_022082.4

Inheritance

ClinVar variants

P:1U:83B:28

Top phenotype

Porokeratosis 8, disseminated superficial actinic type

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr20:62,952,707-62,969,585

External References & Databases

Ensembl (ENSG00000101194)

Transcript & Mutation Effects

hg38 • Region Span ~16.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

disseminated superficial actinic porokeratosisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019212

Submitter: Orphanet

porokeratosis 8, disseminated superficial actinic typeLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014479

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Porokeratosis 8, disseminated superficial actinic typeAD

Manifestation: Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 25180256

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC17A9 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 87

SLC17A9-related disorderTotal: 16

not providedTotal: 11

Porokeratosis 8, disseminated superficial actinic typeTotal: 5

Disseminated superficial actinic porokeratosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022082.4. 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			3 clinvar	15 clinvar		18
missense	1 clinvar		76 clinvar	8 clinvar	2 clinvar	87
nonsense						0
start loss						0
frameshift			1 clinvar	1 clinvar		2
splice donor/acceptor (+/-2bp)			3 clinvar	2 clinvar		5
Total	1	0	83	26	2	112

Highest pathogenic variant AF is 0.000022305081

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022082.4	RefSeq	NP_071365.4	13	MANE Select
ENST00000370351.9	Ensembl	ENSP00000359376.4	13	MANE Select
NM_001302643.2	RefSeq	NP_001289572.2	13	Standard
ENST00000370349.7	Ensembl	ENSP00000359374.3	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

exocytosis
transmembrane transport

Molecular Function

transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370351
Coding exons: 13
Length: 15898
Individuals with no LoFs: 124441
Homozygous LoFs: 2
Heterozygous LoFs: 374
Defined: 124817
p: 0.00151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.29	204	263	0.776	0.0000159	2784
Missense (PolyPhen)		78	96.895	0.80499		1066
Synonymous	-0.728	136	126	1.08	0.00000899	904
Loss of Function	0.0265	25	25.1	0.994	0.00000116	258

Population LoF Frequency

Population	CAF	p-value	Status
African	0.028	0.015	notable
Latino/Admixed American	0.0018	0.0012	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00057	0.00056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00062	0.00059	rare
South Asian	0.00033	0.00029	rare
Other	0.0027	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in vesicular storage and exocytosis of ATP. May accumulate ATP and other nucleotides in secretory vesicles such as adrenal chromaffin granules and synaptic vesicles. {ECO:0000269|PubMed:18375752}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.836
RVIS EVS: 0.38
RVIS percentile EVS: 75.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.624

Gene Damage Prediction

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