GeneBe

SLC10A7

protein-coding

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

Gene summary

Predicted to enable symporter activity. Involved in bone development; heparin proteoglycan biosynthetic process; and intracellular calcium ion homeostasis. Located in Golgi apparatus; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:
  • C4orf13

MANE transcript

NM_001029998.6

Inheritance

AR

ClinVar variants

P:9U:42B:15

Top phenotype

Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr4:146,253,975-146,522,372

External References & Databases

Ensembl (ENSG00000120519)NCBI Gene (84068)OMIM (611459)HGNC:23088GenCCUniProt (Q0GE19)AlphaFoldClinVar (SLC10A7)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~268.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032703

Submitter: Labcorp Genetics (formerly Invitae)

short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0032703

Submitter: ClinGen

*SLC10A7*, the gene encoding solute carrier family 10 (sodium/bile acid cotransporter family), member 7, also called Na(+)/bile acid cotransporter 7, SBF-domain containing protein, has been reported in individuals with skeletal dysplasia with amelogenesis imperfecta, also described as short stature, *amelogenesis imperfecta* and skeletal dysplasia with scoliosis (SSASKS, OMIM #618363; Ashikov et al. 2018. PMID: 29878199; Dubail et al. 2018. PMID: 30082715; Laugel-Haushalter et al. 2019. PMID: 31191616). The SLC10 family (Solute Carrier Family 10), known as bile acid and steroid transport family containing the signature SBF (Sodium Bile transporter Family - Pfam PF017) domain, is composed of seven members. The initially identified family members function as Na+ and bile acid cotransporters while the biological functions of the other members are still unclear. SLC10A7, the last member of SLC10 protein family, does not exhibit any transport activity for the typical SLC10 substrates, and is an orphan carrier (Durin et al. 2022. PMID: 34999954). SLC10A7 is ubiquitously expressed in human tissues and localizes to different cellular compartments of the secretory pathway, especially the Golgi complex, and is hypothesized to be a negative regulator of intracellular calcium signaling (Karakus et al. 2020. PMID: 32350310). SLC10A7-CDG patients have overrepresented high-mannose N-glycans, only composed of N-acetylglucosamine and mannose residues, and decreased sialylation degree of complex (mature) N-glycans (Ashikov et al. 2018. PMID: 29878199) and decreased heparan-sulfate (HS) and accumulation of chondroitin sulfate (CS) at proximity of chondrocytes in KO mice (Dubail et al. 2018. PMID: 30082715). SLC10A7 is suggested to be a key Golgi transmembrane protein maintaining the tight regulation of calcium homeostasis in the ER and Golgi compartments, both essential for glycosylation (Durin et al. 2025. PubMed ID: 39779512). To date, 11 variants in *SLC10A7* (OMIM: 611459) including four missense, four nonsense, three splicing variants, and one entire gene deletion variant have been reported or submitted to ClinVar as pathogenic or likely pathogenic as causative for SSASKS. This curation includes nine variants (including four missense, two nonsense, and three splicing variants) from nine probands in four publications (Ashikov et al. 2018. PMID: 29878199; Dubail et al. 2018. PMID: 30082715; Laugel-Haushalter et al. 2019. PMID: 31191616; Zhang et al. 2023. PMID: 38037133). The score for genetic evidence has reached the maximum of 12 pts. The mechanism of pathogenicity appears to be loss of function. This gene-disease relationship is also supported by experimental evidence. This includes the non-human animal models of zebrafish and mouse with *SLC10A7* deficiency, which recapitulate the clinical and histopathological features of the disease in humans (Ashikov et al. 2018. PMID: 29878199; Dubail et al. 2018. PMID: 30082715). In addition, biochemical functional studies in isogenic *SLC10A7* KO HAP1 cells and SLC10A7-CDG patient fibroblasts have shown loss of SLC10A7 leads to severe Golgi O‑GalNAc glycosylation defects and increased ER and Golgi calcium contents (Durin et al. 2025. PubMed ID: 39779512). (Experimental evidence – 4.5 points). In summary, there is definitive evidence supporting the relationship between *SLC10A7* and autosomal recessive SSASKS/SLC10A7-CDG. This has been repeatedly demonstrated in both the research and clinical diagnostic settings. This classification was approved by the ClinGen Congenital Disorders of Glycosylation GCEP on November 17, 2025 (SOP Version v11).

short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0032703

Submitter: G2P

short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0032703

Submitter: Ambry Genetics

short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032703

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisAR

Manifestation: Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic

Intervention: General

Rationale: 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

Refs: 29878199; 30082715Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC10A7 variants in ClinVar

5 Conditions Cataloged
not providedTotal: 46
Inborn genetic diseasesTotal: 30
SLC10A7-related disorderTotal: 10
not specifiedTotal: 9
Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosisTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001029998.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
8
clinvar
 10
missense
3
clinvar
39
clinvar
5
clinvar
2
clinvar
 49
nonsense
3
clinvar
 3
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
 3
Total724213266

Highest pathogenic variant AF is 0.000051563376

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001029998.6RefSeqNP_001025169.112MANE Select
ENST00000335472.12EnsemblENSP00000334594.812MANE Select
NM_001300842.3RefSeqNP_001287771.112Standard
NM_001317816.2RefSeqNP_001304745.111Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
slc10a7Danio rerio

Structure: palate

Quality: increased width

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • sodium ion transport
  • transmembrane transport

Molecular Function

  • symporter activity

Cellular Component

  • endoplasmic reticulum membrane
  • plasma membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000335472
Coding exons
12
Length
267997
Individuals with no LoFs
125731
Homozygous LoFs
0
Heterozygous LoFs
17
Defined
125748
p
0.0000676
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.341251750.7150.000008192193
Missense (PolyPhen)3351.1220.64551651
Synonymous0.2626365.70.9590.00000347696
Loss of Function1.571017.00.5907.17e-7219

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.0000910.000087rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000710.000070rare
South Asian0.000100.000098rare
Other00.0absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.0842

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.