GML

glycosylphosphatidylinositol anchored molecule like, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 8:142834246-142916506

Links

ENSG00000104499 ∙ NCBI:2765 ∙ OMIM:602370 ∙ HGNC:4375 ∙ Uniprot:Q99445 ∙ 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 GML gene.

• Inborn genetic diseases (7 variants)
• Autism (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GML 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					1	1
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	1

Variants in GML

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

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

Position	Type	Phenotype	Significance	ClinVar
8-142840465-A-G		Autism • not specified	Likely benign (May 17, 2023)
8-142840483-G-T		not specified	Uncertain significance (Aug 02, 2022)
8-142840501-C-T		not specified	Uncertain significance (Jul 31, 2023)
8-142840503-C-T			Benign (Jun 28, 2018)
8-142841130-T-G		not specified	Uncertain significance (Aug 02, 2023)
8-142841146-T-G		not specified	Uncertain significance (Dec 13, 2023)
8-142841166-A-G		not specified	Uncertain significance (May 26, 2022)
8-142841214-C-T		not specified	Uncertain significance (May 31, 2023)
8-142841220-C-T		not specified	Uncertain significance (Dec 12, 2023)
8-142841222-A-C		not specified	Uncertain significance (Jan 16, 2024)
8-142846632-G-A		not specified	Uncertain significance (Jan 30, 2024)
8-142872394-C-T		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 13, 2018)
8-142872429-C-T		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Apr 27, 2017)
8-142872444-T-G		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 13, 2018)
8-142872502-A-T		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Benign/Likely benign (Jan 13, 2018)
8-142872521-A-C		Deficiency of steroid 11-beta-monooxygenase • Glucocorticoid-remediable aldosteronism	Benign (Jan 13, 2018)
8-142872603-T-A		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 12, 2018)
8-142872750-C-G		Deficiency of steroid 11-beta-monooxygenase • Glucocorticoid-remediable aldosteronism	Uncertain significance (Jan 13, 2018)
8-142872751-G-A		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 12, 2018)
8-142872783-C-G		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 12, 2018)
8-142872807-C-A		Deficiency of steroid 11-beta-monooxygenase • Glucocorticoid-remediable aldosteronism	Benign (Jan 13, 2018)
8-142872817-AG-A		Congenital adrenal hyperplasia • Glucocorticoid-remediable aldosteronism	Likely benign (Jun 14, 2016)
8-142872823-G-A		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 12, 2018)
8-142872861-C-T		Deficiency of steroid 11-beta-monooxygenase • Glucocorticoid-remediable aldosteronism	Benign/Likely benign (Jan 13, 2018)
8-142872862-G-A		Glucocorticoid-remediable aldosteronism • Deficiency of steroid 11-beta-monooxygenase	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GML	protein_coding	protein_coding	ENST00000220940	3	82260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.218	0.658	125223	6	508	125737	0.00205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00207	91	91.1	0.999	0.00000464	1043
Missense in Polyphen		23	23.852	0.96429		311
Synonymous	1.44	22	32.4	0.678	0.00000175	301
Loss of Function	1.07	1	3.00	0.333	1.26e-7	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0293	0.0293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000568	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000568	0.0000544
South Asian	0.000351	0.000327
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the apoptotic pathway or cell-cycle regulation induced by p53/TP53 after DNA damage.
• Pathway: Cellular response to heat stress;HSF1 activation;Attenuation phase;HSF1-dependent transactivation;Regulation of HSF1-mediated heat shock response;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Recessive Scores

• pRec: 0.0876

Intolerance Scores

• loftool: 0.761
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.0498
• hipred: N
• hipred_score: 0.145

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.101

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gml2

Gene ontology

• Biological process: apoptotic process;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;negative regulation of cell population proliferation
• Cellular component: plasma membrane;extrinsic component of membrane;anchored component of membrane