MSANTD3-TMEFF1

MSANTD3-TMEFF1 readthrough

Basic information

Region (hg38): 9:100442271-100577636

Previous symbols: [ "C9orf30-TMEFF1" ]

Links

ENSG00000251349 ∙ NCBI:100526694 ∙ ∙ HGNC:38838 ∙ ∙ ∙ 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 MSANTD3-TMEFF1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSANTD3-TMEFF1 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			5			5
Total	0	0	5	0	0

Variants in MSANTD3-TMEFF1

This is a list of pathogenic ClinVar variants found in the MSANTD3-TMEFF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-100450647-C-T		not specified	Uncertain significance (Mar 27, 2023)
9-100450716-T-C		not specified	Uncertain significance (Dec 21, 2023)
9-100450956-A-G		not specified	Uncertain significance (Mar 06, 2023)
9-100473554-G-A		not specified	Uncertain significance (Jul 19, 2022)
9-100473555-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-100473630-T-A		not specified	Uncertain significance (Jul 06, 2021)
9-100473671-C-T		not specified	Uncertain significance (Jan 29, 2024)
9-100473707-C-T		not specified	Uncertain significance (Mar 28, 2024)
9-100473724-G-C		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSANTD3-TMEFF1	protein_coding	protein_coding	ENST00000502978	10	135366

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.237	0.763	125723	0	21	125744	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	142	183	0.777	0.00000884	2263
Missense in Polyphen		50	76.67	0.65215		962
Synonymous	0.116	62	63.2	0.981	0.00000336	601
Loss of Function	3.17	5	20.5	0.244	9.90e-7	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.000702	0.000695
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000802	0.0000791
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May inhibit NODAL and BMP signaling during neural patterning (By similarity). May be a tumor suppressor in brain cancers. {ECO:0000250, ECO:0000269|PubMed:12743596}.

Haploinsufficiency Scores

• ghis: 0.401

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

• Cellular component: integral component of membrane