MACC1

MET transcriptional regulator MACC1

Basic information

Region (hg38): 7:20134654-20217404

Links

ENSG00000183742 ∙ NCBI:346389 ∙ OMIM:612646 ∙ HGNC:30215 ∙ Uniprot:Q6ZN28 ∙ 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 MACC1 gene.

• Inborn genetic diseases (37 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MACC1 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						0
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in MACC1

This is a list of pathogenic ClinVar variants found in the MACC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-20140968-A-T		not specified	Uncertain significance (Sep 01, 2021)
7-20140999-T-G		not specified	Uncertain significance (Oct 30, 2023)
7-20141113-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-20154221-C-T		not specified	Likely benign (Dec 05, 2022)
7-20154365-T-G		not specified	Uncertain significance (Jun 11, 2021)
7-20158208-A-G		not specified	Uncertain significance (Oct 25, 2023)
7-20158299-T-C		not specified	Uncertain significance (Jun 09, 2022)
7-20158515-C-A		not specified	Uncertain significance (Sep 22, 2023)
7-20158543-A-C		not specified	Uncertain significance (Jan 17, 2024)
7-20158568-T-C		not specified	Uncertain significance (Jul 08, 2022)
7-20158617-C-T		not specified	Uncertain significance (May 25, 2022)
7-20158625-G-A		not specified	Uncertain significance (Jul 05, 2022)
7-20158727-T-C		not specified	Uncertain significance (Jun 30, 2023)
7-20158780-G-C		not specified	Uncertain significance (Nov 12, 2021)
7-20158964-A-T		not specified	Uncertain significance (Sep 17, 2021)
7-20158971-C-T		not specified	Uncertain significance (Apr 14, 2022)
7-20158973-C-T		not specified	Uncertain significance (Apr 28, 2023)
7-20159000-T-C		not specified	Uncertain significance (Aug 11, 2022)
7-20159007-T-A		not specified	Uncertain significance (Nov 06, 2023)
7-20159016-C-T		not specified	Uncertain significance (Oct 12, 2021)
7-20159201-A-C		not specified	Uncertain significance (Jun 21, 2022)
7-20159357-A-T		not specified	Uncertain significance (May 24, 2023)
7-20159403-A-G		not specified	Uncertain significance (Jun 28, 2023)
7-20159531-A-G		not specified	Uncertain significance (Aug 14, 2023)
7-20159601-A-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MACC1	protein_coding	protein_coding	ENST00000400331	4	82750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.01e-19	0.00653	125464	2	278	125744	0.00111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.29	501	426	1.18	0.0000202	5578
Missense in Polyphen		138	112.32	1.2286		1512
Synonymous	0.279	152	156	0.972	0.00000773	1625
Loss of Function	0.283	29	30.7	0.945	0.00000147	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00310	0.00291
Ashkenazi Jewish	0.00492	0.00328
East Asian	0.00251	0.00250
Finnish	0.000424	0.000416
European (Non-Finnish)	0.000553	0.000545
Middle Eastern	0.00251	0.00250
South Asian	0.00216	0.00213
Other	0.00103	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcription activator for MET and as a key regulator of HGF-MET signaling. Promotes cell motility, proliferation and hepatocyte growth factor (HGF)-dependent scattering in vitro and tumor growth and metastasis in vivo. {ECO:0000269|PubMed:19098908}.

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.987
• rvis_EVS: 1.81
• rvis_percentile_EVS: 96.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.251
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Macc1

Zebrafish Information Network

• Gene name: macc1
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: regulation of signaling receptor activity;positive regulation of transcription by RNA polymerase II;positive regulation of cell division
• Cellular component: nucleus;cytoplasm;mitochondrion
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;growth factor activity