ABCC12

ATP binding cassette subfamily C member 12, the group of ATP binding cassette subfamily C

Basic information

Region (hg38): 16:48080881-48156018

Links

ENSG00000140798 ∙ NCBI:94160 ∙ OMIM:607041 ∙ HGNC:14640 ∙ Uniprot:Q96J65 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC12 gene.

• Inborn genetic diseases (50 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC12 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	2	6
missense			50	3	2	55
nonsense				2		2
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	9	5

Variants in ABCC12

This is a list of pathogenic ClinVar variants found in the ABCC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-48083759-C-G		not specified	Uncertain significance (May 22, 2023)
16-48083763-C-T			Benign (Dec 31, 2019)
16-48083782-G-C		not specified	Uncertain significance (Feb 06, 2023)
16-48083962-G-T		not specified	Uncertain significance (Jan 11, 2023)
16-48083968-C-T		not specified	Uncertain significance (Dec 19, 2023)
16-48084063-A-C		not specified	Uncertain significance (Nov 14, 2023)
16-48085637-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-48085660-C-T		not specified	Uncertain significance (Jun 02, 2023)
16-48085664-T-G		not specified	Uncertain significance (Jan 10, 2023)
16-48087951-G-A		not specified	Uncertain significance (Apr 12, 2022)
16-48087989-T-G			Benign (Dec 31, 2019)
16-48088014-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-48088029-T-C		not specified	Uncertain significance (Jan 17, 2024)
16-48088652-C-T		not specified	Likely benign (Apr 13, 2022)
16-48088653-T-C		not specified	Uncertain significance (May 25, 2022)
16-48088711-A-T		not specified	Uncertain significance (Oct 20, 2021)
16-48088721-T-G		not specified	Uncertain significance (Jul 14, 2022)
16-48088725-G-A		not specified	Uncertain significance (Feb 17, 2023)
16-48091167-T-C		not specified	Uncertain significance (Jan 01, 2023)
16-48091168-C-T			Likely benign (Jan 01, 2023)
16-48091178-G-C		not specified	Uncertain significance (Feb 06, 2023)
16-48091181-C-G		not specified	Uncertain significance (Apr 20, 2023)
16-48096831-G-T			Uncertain significance (Jan 01, 2023)
16-48096858-C-A		not specified	Uncertain significance (Nov 03, 2023)
16-48096873-C-G		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC12	protein_coding	protein_coding	ENST00000311303	29	73046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.57e-49	2.05e-8	117133	123	8492	125748	0.0349

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0921	779	772	1.01	0.0000438	8885
Missense in Polyphen		212	197.63	1.0727		2400
Synonymous	0.417	303	312	0.970	0.0000196	2694
Loss of Function	-0.364	72	68.7	1.05	0.00000360	794

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0840	0.0826
Ashkenazi Jewish	0.0154	0.0154
East Asian	0.0136	0.0136
Finnish	0.0198	0.0195
European (Non-Finnish)	0.0428	0.0425
Middle Eastern	0.0136	0.0136
South Asian	0.0419	0.0412
Other	0.0315	0.0316

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transporter. {ECO:0000250}.
• Pathway: ABC transporters - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0909

Intolerance Scores

• loftool: 0.108
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.07

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcc12

Gene ontology

• Biological process: transmembrane transport
• Cellular component: membrane;integral component of membrane
• Molecular function: ATP binding;ATPase activity, coupled to transmembrane movement of substances