MIER1

protein-coding

MIER1 transcriptional regulator, the group of Myb/SANT domain containing

Gene summary

This gene encodes a protein that was first identified in Xenopus laevis by its role in a mesoderm induction early response (MIER). The encoded protein functions as a transcriptional regulator. Alternatively spliced transcript variants encode multiple isoforms, some of which lack a C-terminal nuclear localization signal. [provided by RefSeq, May 2013]

MANE transcript

NM_001077700.3

Inheritance

—

ClinVar variants

U:62B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr1:66,924,895-66,988,619

External References & Databases

Ensembl (ENSG00000198160)

Transcript & Mutation Effects

hg38 • Region Span ~63.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MIER1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001077700.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			58 clinvar	1 clinvar		59
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	62	2	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001077700.3	RefSeq	NP_001071168.2	14	MANE Select
ENST00000401041.6	Ensembl	ENSP00000383820.1	14	MANE Select
NM_001077701.3	RefSeq	NP_001071169.1	13	Standard
NM_001077702.3	RefSeq	NP_001071170.2	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
histone deacetylation
positive regulation of chromatin silencing
positive regulation of I-kappaB kinase/NF-kappaB signaling

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
RNA polymerase II repressing transcription factor binding
DNA binding
transcription corepressor activity
histone deacetylase activity

Cellular Component

nucleus
nucleoplasm
cytoplasm
transcriptional repressor complex
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401041
Coding exons: 14
Length: 63725
Individuals with no LoFs: 124781
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124795
p: 0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.54	218	292	0.746	0.0000141	3759
Missense (PolyPhen)		48	89.381	0.53703		1231
Synonymous	0.988	84	96.3	0.872	0.00000445	978
Loss of Function	4.17	8	34.4	0.232	0.00000208	403

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00014	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional repressor regulating the expression of a number of genes including SP1 target genes. Probably functions through recruitment of HDAC1 a histone deacetylase involved in chromatin silencing. {ECO:0000269|PubMed:12482978}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.739
RVIS EVS: -0.07
RVIS percentile EVS: 48.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.835

Gene Damage Prediction

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