MTHFSD

methenyltetrahydrofolate synthetase domain containing, the group of RNA binding motif containing

Basic information

Region (hg38): 16:86530178-86555235

Links

ENSG00000103248 ∙ NCBI:64779 ∙ OMIM:616820 ∙ HGNC:25778 ∙ Uniprot:Q2M296 ∙ 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 MTHFSD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTHFSD 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			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	0

Variants in MTHFSD

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

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

Position	Type	Phenotype	Significance	ClinVar
16-86532025-G-C		not specified	Uncertain significance (Jan 30, 2024)
16-86532045-C-G		not specified	Uncertain significance (Jan 08, 2024)
16-86532066-C-A		not specified	Uncertain significance (Apr 25, 2022)
16-86532067-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-86532114-G-A		not specified	Uncertain significance (Apr 18, 2023)
16-86532124-G-A		not specified	Uncertain significance (Oct 17, 2023)
16-86532135-C-T		not specified	Likely benign (Dec 28, 2023)
16-86532142-G-T		not specified	Uncertain significance (Nov 20, 2024)
16-86532184-G-A		not specified	Uncertain significance (Aug 04, 2021)
16-86532217-C-G		not specified	Uncertain significance (Sep 25, 2023)
16-86532219-C-T		not specified	Uncertain significance (Aug 04, 2023)
16-86532232-C-T		not specified	Uncertain significance (Feb 14, 2023)
16-86532271-G-C		not specified	Uncertain significance (Nov 28, 2023)
16-86532273-G-A		not specified	Uncertain significance (Jul 30, 2023)
16-86532313-C-T		not specified	Uncertain significance (Dec 03, 2021)
16-86532324-G-A		not specified	Uncertain significance (Nov 23, 2024)
16-86532367-C-G		not specified	Uncertain significance (Mar 20, 2024)
16-86532379-G-T		not specified	Uncertain significance (Jul 25, 2023)
16-86532418-C-A		not specified	Uncertain significance (Nov 17, 2023)
16-86532429-C-T		not specified	Uncertain significance (Apr 08, 2024)
16-86541747-T-C		not specified	Uncertain significance (Oct 11, 2024)
16-86541773-T-A		not specified	Uncertain significance (Apr 13, 2023)
16-86541774-C-G		not specified	Uncertain significance (Nov 18, 2022)
16-86541812-A-T		not specified	Uncertain significance (Sep 10, 2024)
16-86542115-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTHFSD	protein_coding	protein_coding	ENST00000360900	8	25060

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.60e-12	0.0182	124686	0	115	124801	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.984	245	205	1.19	0.0000121	2405
Missense in Polyphen		113	89.597	1.2612		984
Synonymous	-0.210	90	87.5	1.03	0.00000582	791
Loss of Function	-0.500	16	14.0	1.14	7.43e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000778	0.000778
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000363	0.000362
Middle Eastern	0.0000557	0.0000556
South Asian	0.00131	0.00131
Other	0.00116	0.00115

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0913

Intolerance Scores

• loftool: 0.928
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94.02

Haploinsufficiency Scores

• pHI: 0.0975
• hipred: N
• hipred_score: 0.219
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mthfsd

Gene ontology

• Cellular component: cytoplasm
• Molecular function: RNA binding