SLC9C2

solute carrier family 9 member C2 (putative), the group of Solute carrier family 9

Basic information

Region (hg38): 1:173500459-173603072

Previous symbols: [ "SLC9A11" ]

Links

ENSG00000162753 ∙ NCBI:284525 ∙ ∙ HGNC:28664 ∙ Uniprot:Q5TAH2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC9C2 gene.

• Inborn genetic diseases (30 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9C2 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						0
missense			26	5	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	5	1

Variants in SLC9C2

This is a list of pathogenic ClinVar variants found in the SLC9C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-173506858-G-C		not specified	Uncertain significance (Feb 23, 2023)
1-173507031-A-T		not specified	Uncertain significance (Dec 01, 2022)
1-173509656-G-A		not specified	Likely benign (Mar 02, 2023)
1-173517559-A-G		not specified	Likely benign (Jan 04, 2022)
1-173517577-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-173521384-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-173521386-A-T		not specified	Uncertain significance (Jun 27, 2022)
1-173524028-T-C		not specified	Uncertain significance (Aug 04, 2023)
1-173524091-G-A		not specified	Uncertain significance (Jun 22, 2023)
1-173524849-G-A		not specified	Uncertain significance (Jan 07, 2022)
1-173524867-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-173529924-A-T		not specified	Uncertain significance (Dec 03, 2021)
1-173529943-G-T		not specified	Uncertain significance (Nov 30, 2021)
1-173530035-A-T		not specified	Uncertain significance (Oct 26, 2022)
1-173530042-T-A		not specified	Likely benign (Mar 01, 2023)
1-173533648-C-T		not specified	Likely benign (Dec 13, 2023)
1-173533671-G-A		not specified	Uncertain significance (Jun 13, 2022)
1-173533759-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-173534567-T-C		not specified	Uncertain significance (Jul 12, 2022)
1-173535888-T-C		not specified	Uncertain significance (Sep 16, 2021)
1-173535895-T-C		not specified	Likely benign (Dec 11, 2023)
1-173535939-T-C			Uncertain significance (Dec 21, 2022)
1-173536949-G-C		not specified	Uncertain significance (Oct 17, 2023)
1-173537020-C-G		not specified	Uncertain significance (Apr 20, 2023)
1-173547768-T-C		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9C2	protein_coding	protein_coding	ENST00000367714	27	102631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000195	1.00	125697	0	41	125738	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	429	564	0.761	0.0000272	7421
Missense in Polyphen		120	165.81	0.72373		2400
Synonymous	1.69	153	182	0.841	0.00000903	2002
Loss of Function	4.87	18	58.1	0.310	0.00000264	822

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000301
Ashkenazi Jewish	0.000427	0.000397
East Asian	0.000170	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000158	0.000149
Middle Eastern	0.000170	0.000163
South Asian	0.000210	0.000196
Other	0.000180	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pH regulation. {ECO:0000250}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.0599

Intolerance Scores

• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.63

Haploinsufficiency Scores

• pHI: 0.0374
• hipred: N
• hipred_score: 0.214

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of intracellular pH;potassium ion transmembrane transport;sodium ion import across plasma membrane;proton transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: sodium:proton antiporter activity;potassium:proton antiporter activity