SLC4A2

solute carrier family 4 member 2, the group of Solute carrier family 4

Basic information

Region (hg38): 7:151057209-151076526

Previous symbols: [ "EPB3L1", "AE2" ]

Links

ENSG00000164889 ∙ NCBI:6522 ∙ OMIM:109280 ∙ HGNC:11028 ∙ Uniprot:P04920 ∙ 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
Osteopetrosis, autosomal recessive 9	AR	Renal	An individual has been described with renal failure requiring renal transplant, and awareness may enable early diagnosis and management of renal issues and sequelae	Musculoskeletal; Renal	34668226

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC4A2 gene.

• Inborn genetic diseases (44 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC4A2 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				3	2	5
missense			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	44	5	2

Variants in SLC4A2

This is a list of pathogenic ClinVar variants found in the SLC4A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-151057808-T-C			Uncertain significance (Aug 10, 2022)
7-151062021-G-A		not specified	Uncertain significance (Apr 19, 2023)
7-151064203-C-T			Uncertain significance (-)
7-151064211-G-A			Uncertain significance (-)
7-151064244-G-A			Uncertain significance (-)
7-151064312-C-T			Likely benign (Nov 01, 2022)
7-151064545-C-T			Uncertain significance (-)
7-151064589-G-A		not specified	Uncertain significance (Nov 15, 2023)
7-151064594-C-T		not specified	Uncertain significance (Oct 26, 2021)
7-151064610-G-T		not specified	Uncertain significance (Mar 01, 2023)
7-151064628-G-A			Likely benign (Oct 01, 2023)
7-151064693-G-T		not specified	Uncertain significance (Feb 06, 2024)
7-151064720-C-T		not specified	Uncertain significance (Nov 16, 2021)
7-151064771-C-T			Likely benign (Sep 01, 2023)
7-151064878-C-T		not specified	Uncertain significance (Jun 11, 2021)
7-151064879-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-151064891-G-A		not specified	Uncertain significance (Jan 03, 2024)
7-151064918-T-C		not specified	Uncertain significance (Feb 27, 2024)
7-151064944-G-A		Osteopetrosis, autosomal recessive 9	Pathogenic (Oct 02, 2023)
7-151066522-A-C		not specified	Likely benign (Nov 09, 2022)
7-151066524-G-A		not specified	Uncertain significance (Feb 28, 2024)
7-151066573-G-T		not specified	Uncertain significance (Apr 25, 2023)
7-151066584-G-A			Uncertain significance (-)
7-151066599-C-T		not specified	Uncertain significance (Jun 24, 2022)
7-151066633-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC4A2	protein_coding	protein_coding	ENST00000485713	22	19318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0148	125728	0	16	125744	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	566	803	0.705	0.0000541	7934
Missense in Polyphen		193	362.16	0.53291		3624
Synonymous	0.545	328	341	0.962	0.0000227	2683
Loss of Function	5.56	9	52.5	0.172	0.00000299	550

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000151	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000734	0.0000703
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000348	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plasma membrane anion exchange protein of wide distribution.
• Pathway: Bile secretion - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters (Consensus)

Intolerance Scores

• loftool: 0.0699
• rvis_EVS: -1.77
• rvis_percentile_EVS: 2.32

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.662
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.454

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc4a2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; 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); reproductive system phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; immune system phenotype

Gene ontology

• Biological process: anion transport;spermatogenesis;inorganic anion transport;bicarbonate transport;digestive tract development;regulation of intracellular pH;anion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;focal adhesion;membrane;basolateral plasma membrane;apical plasma membrane
• Molecular function: inorganic anion exchanger activity;anion transmembrane transporter activity;anion:anion antiporter activity;enzyme binding