SLC17A9

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

Basic information

Region (hg38): 20:62952707-62969585

Previous symbols: [ "C20orf59" ]

Links

ENSG00000101194 ∙ NCBI:63910 ∙ OMIM:612107 ∙ HGNC:16192 ∙ Uniprot:Q9BYT1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• disseminated superficial actinic porokeratosis (Supportive), mode of inheritance: AD
• porokeratosis 8, disseminated superficial actinic type (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Porokeratosis 8, disseminated superficial actinic type	AD	General	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	Dermatologic	25180256

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC17A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				7	1	8
missense			24	5	4	33
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)					2	2
splice region				1	1	2
non coding			1	1	1	3
Total	0	0	25	14	8

Variants in SLC17A9

This is a list of pathogenic ClinVar variants found in the SLC17A9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-62952840-C-A		not specified	Likely benign (Feb 16, 2023)
20-62952855-C-T		Porokeratosis 8, disseminated superficial actinic type • not specified	Uncertain significance (May 04, 2022)
20-62952870-G-C		not specified	Uncertain significance (Apr 23, 2024)
20-62952880-A-C		not specified	Uncertain significance (Dec 01, 2022)
20-62952880-A-G		not specified	Uncertain significance (Jul 22, 2022)
20-62953231-C-A		SLC17A9-related disorder	Likely benign (Jul 26, 2019)
20-62956769-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-62956891-C-T		SLC17A9-related disorder	Likely benign (Jan 03, 2019)
20-62956892-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-62956895-A-T		SLC17A9-related disorder	Likely benign (May 22, 2023)
20-62956955-G-A		SLC17A9-related disorder	Likely benign (Dec 31, 2019)
20-62956958-G-A		not specified	Uncertain significance (Dec 19, 2022)
20-62956963-G-T			Benign (Dec 31, 2019)
20-62956964-T-C			Benign (Dec 31, 2019)
20-62957451-G-A		not specified	Uncertain significance (Feb 02, 2022)
20-62957499-G-A		SLC17A9-related disorder	Benign (Sep 27, 2019)
20-62957513-C-T		SLC17A9-related disorder	Benign (Apr 15, 2019)
20-62960561-G-A		not specified	Uncertain significance (Oct 27, 2022)
20-62960578-AT-A			Likely benign (Dec 31, 2019)
20-62962631-C-G		not specified	Likely benign (Feb 27, 2023)
20-62962642-G-A		SLC17A9-related disorder	Likely benign (Apr 03, 2020)
20-62962669-C-T		SLC17A9-related disorder	Likely benign (Nov 20, 2020)
20-62962670-G-A		not specified	Uncertain significance (Nov 02, 2023)
20-62962672-C-T		SLC17A9-related disorder	Likely benign (Jul 16, 2019)
20-62962677-A-G		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A9	protein_coding	protein_coding	ENST00000370351	13	15898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.10e-17	0.00721	124441	2	374	124817	0.00151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	204	263	0.776	0.0000159	2784
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0303	0.0173
Ashkenazi Jewish	0.00	0.00
East Asian	0.000570	0.000556
Finnish	0.0000470	0.0000464
European (Non-Finnish)	0.000624	0.000591
Middle Eastern	0.000570	0.000556
South Asian	0.000328	0.000294
Other	0.00268	0.00181

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.268
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a9
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: exocytosis;transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: transporter activity