GCOM1

GCOM1, MYZAP-POLR2M combined locus

Basic information

Region (hg38): 15:57591908-57714745

Links

ENSG00000137878 ∙ NCBI:145781 ∙ ∙ HGNC:26424 ∙ ∙ ∙ 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 GCOM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCOM1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	4	0	0

Variants in GCOM1

This is a list of pathogenic ClinVar variants found in the GCOM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-57592081-C-T		Inborn genetic diseases	Uncertain significance (Apr 20, 2024)
15-57604287-C-T		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
15-57618084-G-C		Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
15-57618106-C-A		Primary dilated cardiomyopathy • Cardiomyopathy, dilated, 2K	Likely pathogenic (Jan 01, 2017)
15-57618118-A-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
15-57618172-T-A		Inborn genetic diseases	Uncertain significance (May 10, 2024)
15-57618185-A-C		Inborn genetic diseases	Uncertain significance (Jun 05, 2024)
15-57621638-C-T		Cardiomyopathy, dilated, 2K	Pathogenic (Jul 15, 2024)
15-57621643-G-A		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
15-57621671-A-G		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
15-57621677-C-T		Cardiomyopathy, dilated, 2K	Pathogenic (Jul 15, 2024)
15-57621678-G-T		Inborn genetic diseases	Uncertain significance (Apr 22, 2022)
15-57625843-G-A		Inborn genetic diseases	Uncertain significance (Jan 27, 2022)
15-57625843-G-T		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
15-57629711-G-A		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
15-57629714-G-A		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
15-57629732-A-G		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
15-57629735-A-G		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
15-57632440-T-C		Inborn genetic diseases	Uncertain significance (Apr 04, 2024)
15-57632444-C-T		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
15-57633617-A-G		Inborn genetic diseases	Uncertain significance (Nov 03, 2022)
15-57633641-T-C		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
15-57633724-A-C		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
15-57633742-G-A		Cardiomyopathy, dilated, 2K	Pathogenic (Jul 15, 2024)
15-57639459-G-T		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCOM1	protein_coding	protein_coding	ENST00000380569	14	122838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-19	0.0140	125618	0	130	125748	0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.864	326	285	1.14	0.0000153	3601
Missense in Polyphen		98	95.809	1.0229		1243
Synonymous	-2.47	138	106	1.30	0.00000570	990
Loss of Function	0.626	31	35.0	0.886	0.00000187	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00242	0.00242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000901	0.000870
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000364	0.000360
Middle Eastern	0.000901	0.000870
South Asian	0.000197	0.000196
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cellular signaling via Rho-related GTP- binding proteins and subsequent activation of transcription factor SRF (By similarity). Targets TJP1 to cell junctions. In cortical neurons, may play a role in glutaminergic signal transduction through interaction with the NMDA receptor subunit GRIN1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.47

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.168
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular signal transduction
• Cellular component: RNA polymerase II, holoenzyme;cortical actin cytoskeleton;I band