SLC10A7

solute carrier family 10 member 7, the group of Solute carrier family 10

Basic information

Region (hg38): 4:146253975-146522372

Previous symbols: [ "C4orf13" ]

Links

ENSG00000120519 ∙ NCBI:84068 ∙ OMIM:611459 ∙ HGNC:23088 ∙ Uniprot:Q0GE19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis (Moderate), mode of inheritance: AR
• short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis	AR	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	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic	29878199; 30082715

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC10A7 gene.

• not provided (2 variants)
• Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC10A7 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				4	1	5
missense	1		20	6	2	29
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding				1	2	3
Total	2	0	20	11	5

Variants in SLC10A7

This is a list of pathogenic ClinVar variants found in the SLC10A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-146256866-T-C			Likely benign (Oct 14, 2023)
4-146256917-C-A			Uncertain significance (Nov 17, 2022)
4-146258757-C-T		SLC10A7-related disorder	Benign/Likely benign (Jun 01, 2024)
4-146258817-C-T		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
4-146292953-A-C		Inborn genetic diseases	Uncertain significance (Oct 17, 2022)
4-146292972-T-C		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
4-146292986-GA-G			Likely benign (Aug 09, 2022)
4-146292996-T-C		Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis	Pathogenic (Mar 19, 2019)
4-146293940-T-C		SLC10A7-related disorder	Benign (Jan 25, 2024)
4-146293948-C-A			Likely benign (Nov 04, 2021)
4-146293959-T-A			Uncertain significance (Oct 22, 2023)
4-146293974-T-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
4-146293978-G-A		Inborn genetic diseases	Uncertain significance (May 30, 2023)
4-146294018-G-A			Likely benign (Aug 30, 2023)
4-146294038-T-C		SLC10A7-related disorder	Benign/Likely benign (Oct 14, 2023)
4-146305928-G-A		Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis	Pathogenic (Mar 19, 2019)
4-146305981-G-A			Uncertain significance (Nov 08, 2022)
4-146325971-A-G		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
4-146325990-C-T		SLC10A7-related disorder	Likely benign (Dec 11, 2023)
4-146325995-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
4-146326007-TAA-T			Likely benign (Jun 16, 2022)
4-146442774-T-C			Likely benign (Jan 23, 2024)
4-146442812-T-A			Likely benign (Jul 26, 2023)
4-146503841-T-C			Likely benign (Jan 25, 2024)
4-146503857-C-T		Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis	Pathogenic (Mar 19, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC10A7	protein_coding	protein_coding	ENST00000335472	12	267997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000198	0.903	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	125	175	0.715	0.00000819	2193
Missense in Polyphen		33	51.122	0.64551		651
Synonymous	0.262	63	65.7	0.959	0.00000347	696
Loss of Function	1.57	10	17.0	0.590	7.17e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000714	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not show transport activity towards bile acids or steroid sulfates (including taurocholate, cholate, chenodeoxycholate, estrone-3-sulfate, dehydroepiandrosterone sulfate (DHEAS) and pregnenolone sulfate). {ECO:0000269|PubMed:17628207}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.176
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.488
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0842

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc10a7
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; limbs/digits/tail phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: slc10a7
• Affected structure: palate
• Phenotype tag: abnormal
• Phenotype quality: increased width

Gene ontology

• Biological process: sodium ion transport;transmembrane transport
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: symporter activity