TMEM256-PLSCR3

TMEM256-PLSCR3 readthrough (NMD candidate)

Basic information

Region (hg38): 17:7389734-7404097

Links

ENSG00000262481 ∙ NCBI:100529211 ∙ ∙ HGNC:49186 ∙ ∙ ∙ 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 TMEM256-PLSCR3 gene.

• Inborn genetic diseases (8 variants)
• Asphyxiating thoracic dystrophy 3 (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 TMEM256-PLSCR3 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		1	7	1	1	10
Total	0	1	7	1	1

Variants in TMEM256-PLSCR3

This is a list of pathogenic ClinVar variants found in the TMEM256-PLSCR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7390432-A-G		not specified	Uncertain significance (Sep 17, 2021)
17-7390731-C-T		not specified	Uncertain significance (Jun 23, 2021)
17-7392914-G-A			Benign (Jul 30, 2018)
17-7393188-G-C		not specified	Uncertain significance (Nov 12, 2021)
17-7393206-C-T		not specified	Uncertain significance (Sep 15, 2021)
17-7393789-G-A		not specified	Uncertain significance (Aug 13, 2021)
17-7393806-G-A		not specified	Uncertain significance (Sep 14, 2021)
17-7403100-A-G		not specified	Uncertain significance (Jun 17, 2024)
17-7403142-CCACTCAGAGCCTGGTAGTAAAA-C		Asphyxiating thoracic dystrophy 3	Likely pathogenic (-)
17-7403169-G-C		not specified	Uncertain significance (Dec 15, 2023)
17-7403315-G-T		not specified	Uncertain significance (Jun 29, 2023)
17-7403345-G-C		not specified	Uncertain significance (Dec 12, 2023)
17-7403347-G-T		not specified	Uncertain significance (May 28, 2024)
17-7404029-G-A		not specified	Uncertain significance (Mar 19, 2024)
17-7404048-C-A		not specified	Uncertain significance (Jul 30, 2024)
17-7404074-G-A		not specified	Likely benign (Aug 21, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.617
• ghis: 0.513

Gene Damage Prediction

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

Gene ontology

• Biological process: plasma membrane phospholipid scrambling
• Molecular function: phospholipid scramblase activity