SLC9A7

solute carrier family 9 member A7, the group of Solute carrier family 9

Basic information

Region (hg38): X:46599251-46759118

Links

ENSG00000065923 ∙ NCBI:84679 ∙ OMIM:300368 ∙ HGNC:17123 ∙ Uniprot:Q96T83 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, X-linked 108 (Limited), mode of inheritance: XLR
• intellectual developmental disorder, X-linked 108 (Strong), mode of inheritance: XL
• non-syndromic X-linked intellectual disability (Supportive), mode of inheritance: XL
• intellectual developmental disorder, X-linked 108 (Limited), mode of inheritance: XL
• intellectual developmental disorder, X-linked 108 (Limited), mode of inheritance: XL
• intellectual developmental disorder, X-linked 108 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 108	XL	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	Craniofacial; Musculoskeletal; Neurologic	30335141

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC9A7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9A7 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	17	8	26
missense		1	74	1	1	77
nonsense						0
start loss						0
frameshift						0
inframe indel			6	1		7
splice donor/acceptor (+/-2bp)			2			2
splice region			3	4	1	8
non coding			1	8	3	12
Total	0	1	84	27	12

Variants in SLC9A7

This is a list of pathogenic ClinVar variants found in the SLC9A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-46606957-CATT-C			Uncertain significance (Oct 20, 2023)
X-46606962-T-A		Intellectual developmental disorder, X-linked 108	Uncertain significance (Jun 03, 2022)
X-46606966-C-G		not specified	Uncertain significance (Oct 25, 2024)
X-46606986-G-A		not specified	Uncertain significance (Nov 29, 2021)
X-46606992-C-T		Intellectual developmental disorder, X-linked 108	Uncertain significance (-)
X-46606993-G-A			Uncertain significance (Sep 01, 2022)
X-46606998-G-C		not specified	Uncertain significance (Jul 27, 2021)
X-46607045-C-T			Benign (Oct 22, 2021)
X-46607060-T-C		SLC9A7-related disorder	Benign (Dec 13, 2023)
X-46607064-C-T		not specified	Uncertain significance (Jun 28, 2022)
X-46607082-G-A			Uncertain significance (Aug 09, 2022)
X-46607089-C-T			Likely benign (Jan 01, 2024)
X-46607090-G-A			Likely benign (Aug 03, 2023)
X-46607096-C-T			Likely benign (Feb 01, 2022)
X-46607097-G-A			Uncertain significance (Nov 02, 2022)
X-46607134-C-T		Intellectual developmental disorder, X-linked 108	Uncertain significance (Nov 15, 2021)
X-46607135-G-A			Uncertain significance (Apr 14, 2022)
X-46607147-C-T			Likely benign (Mar 12, 2022)
X-46607148-A-G			Uncertain significance (Jun 05, 2024)
X-46607214-C-A			Likely benign (Jun 29, 2022)
X-46613278-G-T			Likely benign (May 08, 2023)
X-46613289-A-G			Uncertain significance (Nov 15, 2023)
X-46613307-G-C		not specified	Likely benign (Jun 10, 2024)
X-46613314-CAT-TGTA			Uncertain significance (Jan 07, 2024)
X-46613320-G-A			Uncertain significance (Feb 26, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9A7	protein_coding	protein_coding	ENST00000328306	17	153738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00648	125733	3	9	125745	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	177	276	0.641	0.0000220	4716
Missense in Polyphen		35	71.09	0.49234		1291
Synonymous	0.179	117	119	0.979	0.0000106	1462
Loss of Function	4.14	2	23.8	0.0839	0.00000177	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000136	0.0000992
East Asian	0.000303	0.000217
Finnish	0.0000630	0.0000462
European (Non-Finnish)	0.0000618	0.0000439
Middle Eastern	0.000303	0.000217
South Asian	0.0000535	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates electroneutral exchange of protons for Na(+) and K(+) across endomembranes. May contribute to Golgi volume and cation homeostasis. {ECO:0000269|PubMed:11279194}.
• Pathway: Sodium/Proton exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.270
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.552
• hipred: Y
• hipred_score: 0.728
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc9a7

Gene ontology

• Biological process: ion transport;regulation of pH;regulation of intracellular pH;potassium ion transmembrane transport;sodium ion import across plasma membrane;proton transmembrane transport
• Cellular component: Golgi membrane;trans-Golgi network;plasma membrane;integral component of membrane;intracellular membrane-bounded organelle;recycling endosome;recycling endosome membrane
• Molecular function: protein binding;sodium:proton antiporter activity;potassium:proton antiporter activity;protein homodimerization activity