TMEM256

transmembrane protein 256

Basic information

Region (hg38): 17:7402975-7404097

Previous symbols: [ "C17orf61" ]

Links

ENSG00000205544 ∙ NCBI:254863 ∙ OMIM:617779 ∙ HGNC:28618 ∙ Uniprot:Q8N2U0 ∙ 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 TMEM256 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM256 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in TMEM256

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

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

Position	Type	Phenotype	Significance	ClinVar
17-7403100-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)
17-7404074-G-A		not specified	Likely benign (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM256	protein_coding	protein_coding	ENST00000302422	4	1163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000615	0.503	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.183	54	57.9	0.932	0.00000263	695
Missense in Polyphen		12	14.474	0.82908		185
Synonymous	0.488	24	27.2	0.881	0.00000140	238
Loss of Function	0.258	5	5.66	0.883	2.39e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000554	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.000165	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 78.95

Haploinsufficiency Scores

• pHI: 0.255
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem256
• Phenotype: skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); limbs/digits/tail phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane;extracellular exosome
• Molecular function: molecular_function