SLC4A10

solute carrier family 4 member 10, the group of Solute carrier family 4

Basic information

Region (hg38): 2:161424332-161985282

Links

ENSG00000144290 ∙ NCBI:57282 ∙ OMIM:605556 ∙ HGNC:13811 ∙ Uniprot:Q6U841 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with hypotonia and characteristic brain abnormalities	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	Craniofacial; Neurologic	37459438; 38054405

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC4A10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC4A10 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	6	5	12
missense			52	1		53
nonsense		2	3			5
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1	2			3
splice region				1		1
non coding					1	1
Total	0	3	58	7	6

Variants in SLC4A10

This is a list of pathogenic ClinVar variants found in the SLC4A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-161624525-A-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
2-161624534-C-T			Uncertain significance (Apr 19, 2023)
2-161708815-T-G		SLC4A10-related disorder	Benign (Feb 21, 2019)
2-161770999-T-C			Likely benign (Dec 11, 2018)
2-161771024-A-C		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
2-161771055-G-A		SLC4A10-related disorder	Uncertain significance (Apr 11, 2023)
2-161804490-G-C		Inborn genetic diseases	Uncertain significance (May 14, 2024)
2-161804500-G-C		Inborn genetic diseases	Uncertain significance (Sep 21, 2023)
2-161804509-G-A		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
2-161804529-A-G		SLC4A10-related disorder	Uncertain significance (May 04, 2023)
2-161804556-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
2-161839818-C-T		Inborn genetic diseases	Uncertain significance (Aug 17, 2021)
2-161839846-A-G		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
2-161839848-A-G		not specified	Uncertain significance (Feb 23, 2017)
2-161839852-C-A		Inborn genetic diseases	Uncertain significance (Mar 11, 2022)
2-161839904-C-T			Benign (May 07, 2018)
2-161853627-GA-G		Neurodevelopmental disorder with hypotonia and characteristic brain abnormalities	Pathogenic (Mar 08, 2024)
2-161855017-G-T			Uncertain significance (Mar 25, 2024)
2-161855086-C-G		Inborn genetic diseases	Uncertain significance (May 27, 2022)
2-161862924-C-T		Inborn genetic diseases	Uncertain significance (Jun 13, 2024)
2-161862940-A-G		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
2-161862942-G-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
2-161862954-C-T			Uncertain significance (Sep 27, 2023)
2-161862963-C-T		Neurodevelopmental disorder with hypotonia and characteristic brain abnormalities	Pathogenic (Mar 08, 2024)
2-161862978-A-T			Uncertain significance (Dec 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC4A10	protein_coding	protein_coding	ENST00000446997	26	560950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.134	0.866	125435	0	29	125464	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.84	312	570	0.548	0.0000283	7291
Missense in Polyphen		100	314.12	0.31835		4005
Synonymous	0.163	197	200	0.985	0.0000101	2120
Loss of Function	5.38	14	58.3	0.240	0.00000303	730

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000537
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.000239	0.000231
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000728	0.0000653
Other	0.000175	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Electrogenic sodium/bicarbonate cotransporter in exchange for intracellular chloride. Plays an important role in regulating intracellular pH (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.770
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.805
• hipred: Y
• hipred_score: 0.771
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc4a10
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: sodium ion transport;chloride transport;response to light stimulus;post-embryonic development;bicarbonate transport;pyramidal neuron development;multicellular organism growth;locomotory exploration behavior;brain morphogenesis;regulation of intracellular pH;anion transmembrane transport;proton transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane;basolateral plasma membrane;neuronal cell body;apical dendrite;basal dendrite;CA3 pyramidal cell dendrite
• Molecular function: inorganic anion exchanger activity;sodium:bicarbonate symporter activity;anion:anion antiporter activity