ABCC6

ATP binding cassette subfamily C member 6, the group of ATP binding cassette subfamily C

Basic information

Region (hg38): 16:16149564-16223522

Previous symbols: [ "ARA", "PXE" ]

Links

ENSG00000091262 ∙ NCBI:368 ∙ OMIM:603234 ∙ HGNC:57 ∙ Uniprot:O95255 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• arterial calcification, generalized, of infancy, 2 (Definitive), mode of inheritance: AR
• autosomal recessive inherited pseudoxanthoma elasticum (Definitive), mode of inheritance: AR
• autosomal recessive inherited pseudoxanthoma elasticum (Supportive), mode of inheritance: AR
• arterial calcification of infancy (Supportive), mode of inheritance: AD
• autosomal recessive inherited pseudoxanthoma elasticum (Strong), mode of inheritance: AR
• autosomal recessive inherited pseudoxanthoma elasticum (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pseudoxanthoma elasticum (including Pseudoxanthoma elasticum, forme fruste)	AD/AR/Digenic	Cardiovascular; Hematologic; Ophthalmologic	Preventive measures (eg, weight control, avoidance of smoking, and medical management of hypertension and hypercholesterolemia) related to cardiovascular risk factors may be beneficial by decreasing contributory factors related to atherosclerosis; Awareness may allow surveillance for and early detection and treatment of cardiovascular (eg, surgical interventions related to vascular disease) and hematologic manifestations (eg, interventions related to GI bleeding); Standard treatment for macular degeneration (including intraocular injection of anti-angiogenic drugs) may be beneficial, and awareness of ophthalmologic aspects may allow early detection and treatment; Circumstances such as contact sports and the use of medications that increase the risk of GI bleeding should be avoided	Cardiovascular; Dermatologic; Hematologic; Ophthalmologic	14068068; 3652487; 3342167; 2012127; 1600795; 8413390; 10619263; 10835643; 10835642; 10811882; 11209132; 15098239; 16086317; 18157818; 18800149; 19298904; 20034067; 20075945; 20301292; 21210805; 21386758; 21671388; 22209248; 23675997; 23746223; 23935882; 23968982; 23978319; 24008425; 24749718
In "recessive" forms, heterozygotes may have mild manifestations; Digenic inheritance (with GGCX) has been reported

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC6 gene.

• not provided (1059 variants)
• Autosomal recessive inherited pseudoxanthoma elasticum (264 variants)
• Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste;Arterial calcification, generalized, of infancy, 2 (98 variants)
• Arterial calcification, generalized, of infancy, 2 (71 variants)
• Pseudoxanthoma elasticum, forme fruste (63 variants)
• Inborn genetic diseases (55 variants)
• Arterial calcification, generalized, of infancy, 2;Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste (42 variants)
• not specified (39 variants)
• ABCC6-related condition (27 variants)
• Pseudoxanthoma elasticum, forme fruste;Autosomal recessive inherited pseudoxanthoma elasticum;Arterial calcification, generalized, of infancy, 2 (24 variants)
• Pseudoxanthoma elasticum, forme fruste;Arterial calcification, generalized, of infancy, 2;Autosomal recessive inherited pseudoxanthoma elasticum (21 variants)
• Arterial calcification, generalized, of infancy, 2;Pseudoxanthoma elasticum, forme fruste;Autosomal recessive inherited pseudoxanthoma elasticum (19 variants)
• See cases (4 variants)
• Abnormality of the eye (2 variants)
• ABCC6-related disorder (2 variants)
• Stroke disorder (2 variants)
• Finnish congenital nephrotic syndrome (1 variants)
• Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste (1 variants)
• Cutis laxa;Papule (1 variants)
• Low-set, posteriorly rotated ears (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC6 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			6	242	17	265
missense	24	35	435	29	12	535
nonsense	22	7	1			30
start loss						0
frameshift	24	15	4			43
inframe indel	1	3	6			10
splice donor/acceptor (+/-2bp)	9	9	3			21
splice region	1	3	31	47	2	84
non coding			6	102	38	146
Total	80	69	461	373	67

Highest pathogenic variant AF is 0.00113

Variants in ABCC6

This is a list of pathogenic ClinVar variants found in the ABCC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-16150095-C-T		Autosomal recessive inherited pseudoxanthoma elasticum • Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste;Arterial calcification, generalized, of infancy, 2 • ABCC6-related disorder	Likely benign (Jan 19, 2022)
16-16150116-C-T		Autosomal recessive inherited pseudoxanthoma elasticum • Pseudoxanthoma elasticum, forme fruste • Arterial calcification, generalized, of infancy, 2	Benign (Dec 05, 2021)
16-16150127-CCTGGCT-C			Uncertain significance (May 15, 2022)
16-16150144-C-T		Autosomal recessive inherited pseudoxanthoma elasticum	Likely pathogenic (Mar 01, 2021)
16-16150155-G-A			Uncertain significance (Mar 26, 2022)
16-16150156-C-T			Uncertain significance (Mar 31, 2022)
16-16150158-A-G			Uncertain significance (Jan 23, 2020)
16-16150161-C-G			Uncertain significance (Apr 24, 2023)
16-16150163-G-A			Likely benign (Oct 13, 2022)
16-16150168-A-G		Pseudoxanthoma elasticum, forme fruste;Autosomal recessive inherited pseudoxanthoma elasticum;Arterial calcification, generalized, of infancy, 2	Uncertain significance (Oct 13, 2022)
16-16150169-C-G		Arterial calcification, generalized, of infancy, 2;Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste	Likely benign (Sep 07, 2021)
16-16150172-G-A			Benign (Dec 11, 2023)
16-16150174-CCTTCTGGGCCAG-C			Uncertain significance (Feb 17, 2021)
16-16150187-C-G			Likely benign (Nov 01, 2022)
16-16150196-C-T			Likely benign (Nov 22, 2022)
16-16150197-G-A		Autosomal recessive inherited pseudoxanthoma elasticum • Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste;Arterial calcification, generalized, of infancy, 2 • ABCC6-related disorder	Uncertain significance (Nov 08, 2022)
16-16150197-G-T		Pseudoxanthoma elasticum, forme fruste;Autosomal recessive inherited pseudoxanthoma elasticum;Arterial calcification, generalized, of infancy, 2	Uncertain significance (May 30, 2022)
16-16150199-G-T			Uncertain significance (Jan 27, 2022)
16-16150200-C-G			Uncertain significance (Feb 23, 2022)
16-16150204-C-T		Autosomal recessive inherited pseudoxanthoma elasticum • Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste;Arterial calcification, generalized, of infancy, 2	Uncertain significance (Oct 17, 2022)
16-16150205-G-A			Likely benign (Nov 27, 2023)
16-16150210-CT-C		Autosomal recessive inherited pseudoxanthoma elasticum	Likely pathogenic (Mar 02, 2021)
16-16150211-T-C			Likely benign (Jan 19, 2023)
16-16150220-C-T			Benign (Jan 22, 2024)
16-16150221-C-T		Autosomal recessive inherited pseudoxanthoma elasticum	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC6	protein_coding	protein_coding	ENST00000205557	31	74595

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.62e-35	0.00158	125040	0	708	125748	0.00282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	926	837	1.11	0.0000531	9576
Missense in Polyphen		222	216.8	1.024		2380
Synonymous	-1.09	391	365	1.07	0.0000239	3223
Loss of Function	1.36	60	72.5	0.828	0.00000361	781

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00236	0.00235
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00440	0.00436
Finnish	0.00431	0.00431
European (Non-Finnish)	0.00378	0.00376
Middle Eastern	0.00440	0.00436
South Asian	0.000916	0.000915
Other	0.00278	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: May participate directly in the active transport of drugs into subcellular organelles or influence drug distribution indirectly. Transports glutathione conjugates as leukotriene-c4 (LTC4) and N-ethylmaleimide S-glutathione (NEM-GS). {ECO:0000269|PubMed:11880368}.
• Disease: DISEASE: Pseudoxanthoma elasticum (PXE) [MIM:264800]: A multisystem disorder characterized by accumulation of mineralized and fragmented elastic fibers in the skin, vascular walls, and Burch membrane in the eye. Clinically, patients exhibit characteristic lesions of the posterior segment of the eye including peau d'orange, angioid streaks, and choroidal neovascularizations, of the skin including soft, ivory colored papules in a reticular pattern that predominantly affect the neck and large flexor surfaces, and of the cardiovascular system with peripheral and coronary arterial occlusive disease as well as gastrointestinal bleedings. {ECO:0000269|PubMed:10811882, ECO:0000269|PubMed:10835642, ECO:0000269|PubMed:10954200, ECO:0000269|PubMed:11427982, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11702217, ECO:0000269|PubMed:11880368, ECO:0000269|PubMed:15086542, ECO:0000269|PubMed:15098239, ECO:0000269|PubMed:15459974, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:17617515, ECO:0000269|PubMed:19339160, ECO:0000269|PubMed:20034067, ECO:0000269|PubMed:25615550}. Note=The disease is caused by mutations affecting the gene represented in this entry. Homozygous or compound heterozygous ABCC6 mutations have been found in the overwhelming majority of cases. Individuals carrying heterozygous mutations express limited manifestations of the pseudoxanthoma elasticum phenotype.; DISEASE: Arterial calcification of infancy, generalized, 2 (GACI2) [MIM:614473]: A severe autosomal recessive disorder characterized by calcification of the internal elastic lamina of muscular arteries and stenosis due to myointimal proliferation. The disorder is often fatal within the first 6 months of life because of myocardial ischemia resulting in refractory heart failure. {ECO:0000269|PubMed:22209248}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: ABC transporters - Homo sapiens (human);Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Intolerance Scores

• loftool: 0.0194
• rvis_EVS: 0.63
• rvis_percentile_EVS: 83.54

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.492
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcc6
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; vision/eye phenotype; renal/urinary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: abcc6b.2
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: visual perception;response to drug;transmembrane transport;ATP hydrolysis coupled anion transmembrane transport
• Cellular component: nucleus;vacuolar membrane;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;basolateral plasma membrane;apical plasma membrane;lateral plasma membrane
• Molecular function: transporter activity;ATP binding;ATPase activity, coupled to transmembrane movement of substances;ATPase-coupled anion transmembrane transporter activity