SLC30A9

solute carrier family 30 member 9, the group of Solute carrier family 30

Basic information

Region (hg38): 4:41990501-42090461

Previous symbols: [ "C4orf1" ]

Links

ENSG00000014824 ∙ NCBI:10463 ∙ OMIM:604604 ∙ HGNC:1329 ∙ Uniprot:Q6PML9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (Moderate), mode of inheritance: AR
• psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (Supportive), mode of inheritance: AR
• psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Birk-Landau-Perez syndrome	AR	Renal	Individuals have been described with childhood-onset renal insufficiency (including hyperkalemia and hypertension) and awaereness may allow early identification and management	Neurologic; Renal	28334855

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC30A9 gene.

• Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (12 variants)
• Inborn genetic diseases (9 variants)
• not provided (4 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A9 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					2	2
missense			13		2	15
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel	1					1
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding					2	2
Total	1	3	13	0	6

Highest pathogenic variant AF is 0.0000263

Variants in SLC30A9

This is a list of pathogenic ClinVar variants found in the SLC30A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-41990660-C-G		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Benign (Jul 15, 2021)
4-41990684-C-G		See cases	Uncertain significance (Apr 05, 2020)
4-41990690-TA-T		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Conflicting classifications of pathogenicity (Jan 03, 2022)
4-41990702-C-T		SLC30A9-related disorder	Likely benign (Aug 28, 2019)
4-41990735-G-C		SLC30A9-related disorder	Benign (Apr 01, 2019)
4-41990736-G-GCC		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Likely pathogenic (-)
4-42001654-A-G		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Benign (Jul 15, 2021)
4-42001684-A-T		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
4-42001758-A-T		SLC30A9-related disorder	Benign (Dec 24, 2019)
4-42001818-C-G		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Benign (Jul 15, 2021)
4-42018125-A-G		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Benign (Jul 15, 2021)
4-42020447-C-A		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Benign (Jul 15, 2021)
4-42022965-A-G		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Benign (Jul 15, 2021)
4-42023317-G-A		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Likely pathogenic (Nov 03, 2022)
4-42035302-G-A			Uncertain significance (May 01, 2023)
4-42049391-G-T		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
4-42049480-G-A		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Likely pathogenic (Jan 03, 2022)
4-42060196-A-T		Inborn genetic diseases	Uncertain significance (Dec 04, 2023)
4-42060207-G-A		Inborn genetic diseases	Uncertain significance (Dec 04, 2021)
4-42063005-C-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
4-42063036-G-A		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Uncertain significance (-)
4-42063105-T-C		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
4-42065323-TAGC-T		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Pathogenic (Apr 08, 2023)
4-42067077-A-G		Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Uncertain significance (Dec 14, 2021)
4-42067186-A-G		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A9	protein_coding	protein_coding	ENST00000264451	18	99986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.67e-7	1.00	125718	0	28	125746	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	210	300	0.700	0.0000150	3631
Missense in Polyphen		47	80.935	0.58071		958
Synonymous	0.411	98	103	0.949	0.00000484	1091
Loss of Function	3.11	17	37.5	0.453	0.00000197	462

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000937	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000562	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.0000562	0.0000544
South Asian	0.0000986	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a zinc transporter involved in intracellular zinc homeostasis (PubMed:28334855). Functions as a secondary coactivator for nuclear receptors by cooperating with p160 coactivators subtypes. Plays a role in transcriptional activation of Wnt-responsive genes (By similarity). {ECO:0000250|UniProtKB:Q5IRJ6, ECO:0000269|PubMed:28334855}.
• Pathway: Zinc homeostasis (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.798
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.685
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.681

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a9

Gene ontology

• Biological process: nucleotide-excision repair;zinc ion transport;cellular zinc ion homeostasis;positive regulation of transcription by RNA polymerase II;cation transmembrane transport
• Cellular component: nucleus;endoplasmic reticulum;cytoskeleton;integral component of membrane;cytoplasmic vesicle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;cation transmembrane transporter activity;nuclear receptor binding;nuclear receptor transcription coactivator activity