SLC9C1

solute carrier family 9 member C1, the group of Solute carrier family 9

Basic information

Region (hg38): 3:112140897-112294227

Previous symbols: [ "SLC9A10" ]

Links

ENSG00000172139 ∙ NCBI:285335 ∙ OMIM:612738 ∙ HGNC:31401 ∙ Uniprot:Q4G0N8 ∙ 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 SLC9C1 gene.

• Inborn genetic diseases (42 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9C1 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					1	1
missense			40	5		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	40	5	1

Variants in SLC9C1

This is a list of pathogenic ClinVar variants found in the SLC9C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-112151869-A-G		not specified	Uncertain significance (Aug 21, 2023)
3-112151945-C-T		not specified	Uncertain significance (Sep 17, 2021)
3-112151959-C-T		not specified	Uncertain significance (Sep 30, 2021)
3-112155037-G-A		not specified	Uncertain significance (Dec 19, 2023)
3-112155055-T-TA			Benign (Aug 04, 2017)
3-112167223-A-G		not specified	Uncertain significance (Jan 08, 2024)
3-112167249-A-T		not specified	Uncertain significance (Mar 31, 2023)
3-112167301-G-A		not specified	Uncertain significance (May 23, 2023)
3-112167328-A-T		not specified	Uncertain significance (Sep 22, 2023)
3-112168889-T-C		not specified	Uncertain significance (Feb 16, 2023)
3-112168911-C-G		not specified	Uncertain significance (May 18, 2022)
3-112168929-A-G		not specified	Uncertain significance (Jul 12, 2023)
3-112168954-T-G		not specified	Uncertain significance (Jun 22, 2023)
3-112169013-T-G		not specified	Uncertain significance (Sep 22, 2023)
3-112169205-A-G		not specified	Uncertain significance (Jul 19, 2022)
3-112169283-A-G			Likely benign (Jan 01, 2023)
3-112169290-A-T			Benign/Likely benign (Apr 01, 2023)
3-112169325-A-G		not specified	Uncertain significance (Mar 11, 2024)
3-112179560-A-C		not specified	Uncertain significance (Jan 10, 2022)
3-112179672-A-C		not specified	Uncertain significance (Dec 02, 2022)
3-112180605-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-112199434-T-C		not specified	Uncertain significance (Aug 08, 2023)
3-112199448-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-112202262-T-C			Benign (Dec 31, 2019)
3-112204229-G-A		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9C1	protein_coding	protein_coding	ENST00000305815	28	153372

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-15	0.998	125631	0	116	125747	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0613	570	574	0.993	0.0000273	7753
Missense in Polyphen		128	158.77	0.80621		2338
Synonymous	-0.146	193	190	1.01	0.00000960	2099
Loss of Function	3.01	33	57.7	0.572	0.00000261	824

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00137
Ashkenazi Jewish	0.000354	0.000198
East Asian	0.000473	0.000435
Finnish	0.0000480	0.0000462
European (Non-Finnish)	0.000522	0.000501
Middle Eastern	0.000473	0.000435
South Asian	0.000362	0.000327
Other	0.000849	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sperm-specific sodium/hydrogen exchanger involved in intracellular pH regulation of spermatozoa. Required for sperm motility and fertility. Involved in sperm cell hyperactivation, a step needed for sperm motility which is essential late in the preparation of sperm for fertilization. Required for the expression and bicarbonate regulation of the soluble adenylyl cyclase (sAC) (By similarity). {ECO:0000250}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.0520

Intolerance Scores

• rvis_EVS: 1.63
• rvis_percentile_EVS: 96.07

Haploinsufficiency Scores

• pHI: 0.0356
• 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	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Slc9c1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation;flagellated sperm motility;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;motile cilium
• Molecular function: ion channel activity;sodium:proton antiporter activity;potassium:proton antiporter activity