ST20-MTHFS

ST20-MTHFS readthrough

Basic information

Region (hg38): 15:79845149-79923754

Links

ENSG00000259332 ∙ NCBI:100528021 ∙ ∙ HGNC:44655 ∙ ∙ ∙ 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 ST20-MTHFS gene.

• not provided (38 variants)
• Inborn genetic diseases (5 variants)
• Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST20-MTHFS 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	1	3
missense			13	2	2	17
nonsense	1	1	1			3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region						0
non coding	1		8	9	2	20
Total	2	1	23	14	5

Highest pathogenic variant AF is 0.0000263

Variants in ST20-MTHFS

This is a list of pathogenic ClinVar variants found in the ST20-MTHFS region.

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

Position	Type	Phenotype	Significance	ClinVar
15-79845217-G-A			Uncertain significance (Mar 01, 2022)
15-79845218-T-C			Benign (Jan 30, 2024)
15-79845230-C-T			Benign (Jul 06, 2023)
15-79845257-C-T			Uncertain significance (Aug 24, 2023)
15-79845258-G-A			Likely benign (Jun 03, 2022)
15-79845306-C-G			Likely benign (Oct 06, 2023)
15-79845338-G-A		Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination	Likely pathogenic (Apr 30, 2019)
15-79845388-C-T		Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination	Conflicting classifications of pathogenicity (Dec 22, 2023)
15-79845402-G-A		MTHFS-related disorder	Benign (Nov 10, 2023)
15-79845447-G-A			Likely benign (Apr 07, 2022)
15-79889094-T-C			Uncertain significance (Aug 03, 2022)
15-79889095-G-A			Uncertain significance (May 12, 2022)
15-79889113-C-T			Uncertain significance (Dec 11, 2023)
15-79889117-C-G			Likely benign (Nov 22, 2023)
15-79889137-G-A			Uncertain significance (Aug 04, 2023)
15-79889152-G-A			Uncertain significance (Nov 27, 2023)
15-79889156-T-A		Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination	Pathogenic (Sep 09, 2021)
15-79889179-G-A			Uncertain significance (May 16, 2022)
15-79889189-T-C			Uncertain significance (Aug 31, 2022)
15-79889221-C-T		not specified	Conflicting classifications of pathogenicity (Aug 26, 2022)
15-79889222-G-A			Uncertain significance (Jul 02, 2022)
15-79889227-C-T		not specified	Uncertain significance (Feb 28, 2023)
15-79889228-G-A			Uncertain significance (Aug 31, 2022)
15-79889252-G-A			Uncertain significance (Jul 01, 2022)
15-79889300-T-C			Uncertain significance (Feb 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST20-MTHFS	protein_coding	protein_coding	ENST00000479961	3	78560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00763	0.793	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.558	83	98.6	0.842	0.00000542	1171
Missense in Polyphen		31	38.588	0.80335		444
Synonymous	0.0187	36	36.1	0.996	0.00000196	339
Loss of Function	0.987	4	6.77	0.591	4.70e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: One carbon pool by folate - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Gene ontology

• Biological process: folic acid-containing compound biosynthetic process;tetrahydrofolate interconversion
• Cellular component: mitochondrion
• Molecular function: ATP binding;5-formyltetrahydrofolate cyclo-ligase activity;metal ion binding