GCM1

glial cells missing transcription factor 1

Basic information

Region (hg38): 6:53126961-53148841

Previous symbols: [ "GCMA" ]

Links

ENSG00000137270 ∙ NCBI:8521 ∙ OMIM:603715 ∙ HGNC:4197 ∙ Uniprot:Q9NP62 ∙ 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 GCM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCM1 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				2	3	5
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	3

Variants in GCM1

This is a list of pathogenic ClinVar variants found in the GCM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-53128265-A-T		not specified	Uncertain significance (May 03, 2023)
6-53128269-C-A		not specified	Uncertain significance (Apr 19, 2023)
6-53128337-C-T		not specified	Likely benign (Mar 20, 2024)
6-53128362-T-C			Likely benign (Jun 01, 2022)
6-53128452-T-A		not specified	Uncertain significance (Jan 16, 2024)
6-53128465-C-T		not specified	Uncertain significance (Dec 14, 2023)
6-53128469-T-A		not specified	Uncertain significance (Feb 12, 2024)
6-53128505-A-G		not specified	Uncertain significance (Apr 20, 2023)
6-53128537-A-C		not specified	Uncertain significance (Nov 08, 2022)
6-53128539-G-T		not specified	Uncertain significance (Jan 11, 2023)
6-53128541-T-C		not specified	Uncertain significance (Nov 22, 2022)
6-53128626-C-G		not specified	Uncertain significance (Jul 25, 2023)
6-53128685-C-T		not specified	Uncertain significance (Sep 13, 2023)
6-53128690-C-G		not specified	Uncertain significance (Jun 29, 2022)
6-53128801-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-53128831-T-C		not specified	Uncertain significance (Jan 26, 2022)
6-53128838-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-53128862-T-G		not specified	Uncertain significance (Jul 08, 2022)
6-53128883-C-T		not specified	Uncertain significance (Feb 17, 2022)
6-53130820-C-T		not specified	Uncertain significance (Jan 06, 2023)
6-53130838-C-T		not specified	Uncertain significance (Aug 02, 2022)
6-53130839-G-A			Likely benign (Jun 01, 2022)
6-53130852-G-T		not specified	Uncertain significance (Aug 17, 2022)
6-53130893-C-T			Benign (Mar 29, 2018)
6-53132024-G-A		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCM1	protein_coding	protein_coding	ENST00000259803	5	21866

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00100	125647	0	1	125648	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	181	244	0.741	0.0000138	2887
Missense in Polyphen		21	76.399	0.27487		851
Synonymous	0.451	88	93.5	0.941	0.00000577	808
Loss of Function	4.15	0	20.0	0.00	0.00000104	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor involved in the control of expression of placental growth factor (PGF) and other placenta- specific genes (PubMed:10542267, PubMed:18160678). Binds to the trophoblast-specific element 2 (TSE2) of the aromatase gene enhancer (PubMed:10542267). Binds to the SYDE1 promoter (PubMed:27917469). Has a central role in mediating the differentiation of trophoblast cells along both the villous and extravillous pathways in placental development (PubMed:19219068). {ECO:0000269|PubMed:10542267, ECO:0000269|PubMed:18160678, ECO:0000269|PubMed:19219068, ECO:0000269|PubMed:27917469}.

Recessive Scores

• pRec: 0.187

Intolerance Scores

• loftool: 0.107
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.173
• hipred: Y
• hipred_score: 0.582
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.224

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcm1
• Phenotype: growth/size/body region phenotype; cellular 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); 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); normal phenotype; embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;transcription by RNA polymerase II;anatomical structure morphogenesis;positive regulation of transcription by RNA polymerase II;astrocyte fate commitment;positive regulation of syncytium formation by plasma membrane fusion;branching involved in labyrinthine layer morphogenesis;cell differentiation involved in embryonic placenta development;regulation of cell differentiation involved in embryonic placenta development
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;zinc ion binding;histone deacetylase binding