TMEM260

transmembrane protein 260

Basic information

Region (hg38): 14:56488354-56650606

Previous symbols: [ "C14orf101" ]

Links

ENSG00000070269 ∙ NCBI:54916 ∙ OMIM:617449 ∙ HGNC:20185 ∙ Uniprot:Q9NX78 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• structural heart defects and renal anomalies syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Structural heart defects and renal anomalies syndrome	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Neurologic; Renal	28318500; 34612517

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM260 gene.

• Structural heart defects and renal anomalies syndrome (8 variants)
• not provided (4 variants)
• Type I truncus arteriosus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM260 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			1	8	2	11
missense		2	55	5	4	66
nonsense	4	1				5
start loss						0
frameshift	6	6				12
inframe indel						0
splice donor/acceptor (+/-2bp)	1	2				3
splice region				3	1	4
non coding			4	2	3	9
Total	11	11	60	15	9

Highest pathogenic variant AF is 0.0000526

Variants in TMEM260

This is a list of pathogenic ClinVar variants found in the TMEM260 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-56579947-C-T			Likely benign (May 15, 2018)
14-56579948-CA-C			Likely pathogenic (Mar 01, 2021)
14-56579973-T-C		Inborn genetic diseases	Likely benign (Dec 12, 2023)
14-56579983-CG-C		Structural heart defects and renal anomalies syndrome	Likely pathogenic (Mar 26, 2024)
14-56579989-C-T			Conflicting classifications of pathogenicity (Jul 03, 2023)
14-56580005-G-C		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
14-56580017-G-A		Inborn genetic diseases	Uncertain significance (May 25, 2022)
14-56580021-T-C		Inborn genetic diseases	Uncertain significance (Mar 22, 2023)
14-56580030-T-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2022)
14-56580030-T-C		Inborn genetic diseases	Uncertain significance (Jun 05, 2023)
14-56580047-C-T		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
14-56580050-C-A		TMEM260-related disorder	Benign (May 16, 2023)
14-56580072-C-T		Inborn genetic diseases	Uncertain significance (Jan 18, 2023)
14-56580081-T-A			Likely benign (Mar 29, 2018)
14-56582231-CTTCCTGATAAGTCTTACATTTTACTCCATAGATTCATCACATTGTGTCGTCTTGCCAAAATTATTTTTTGTACCACTTGACACACACAGTTCATTTATGGGCAGGGTGCTTGTGGTGCTTTTCGGGGAGGGGGTAGGAATCTGGCCTTCACTAAATTAGTTTGTACGTGAGTTTATTTCAAAGATACTGTCTTTAACAGATGTGATGTGTGACAGTCTAGTCTAATTAATATTGAGAAGTATGATATAAAGGGAGCTGGTTTTTGTAAAGGTTAAGCATCTGCTGACAACTCTGGGCTTGCCATTAGTTTGTATTGCAGACAACAAAGCCGTGGTTCTCAGACAGGAACGTACTTCAGAATTACCTGGGAAACTTGAGCCCCCAGTGCAAGTGGGTCTTAGTAGATTATGGAATTTGGAGGTGTGGGCAAGGAATCTTCATTTTTAAAAAGCAGGTTAATTCTGATGCAGGTAGACACAACTGAGGAACCTTTCATGTAAAGGGTTGGGAGAAAGCCAAGACTCGGGAAGCTCGAGGTTTTTTTACTATTCCCTTCCTCTTTATCACAATCAATTTAAGAGTAGTATTTCCCTTTAGATCTTTATCAAGGTTACATTTAGAGACGTTGAATGGGGACATCTTTTCTATTTCGATTTTAGTTTAACATTTGATAAGAATTGATGAAAGTTTGTCACATTCCAGATTTATCTTTATAGCAGCAGAAGTCTGGCAAATAATAACAGCACACTGACTTTTCCATGGTAAAAAGAAGTTAGAGAAAAACAGCCTATTTTTCTTAATGTTAAATGTAATTCTGAATACATTTTAAATGGAGGAGAATGAATAGTGACCTTTGAAATTTTGAATTTATGGTGGCTTCGTTACAAAAAGATTACAGGAACAAAAAAATCGAAAATAGTTTGGAGCTAAAGACTTAAGAGCTAATCCATTATGGAGTAAACTATAAAATCATATCCTTTACAGTAGTTAACAAAGGGAACAGTTGTTTGAGACATTGTGAGACCATAAACTATTTAAAAAGAAGCATTTAGGATATAAAATGTGCTGGTTTCTCAGGTGCTCTTGAATATCTCTTAACAAATGTCCTTAAGTAATTGACTTAATCTGTCTTCAGGTGCCCTTATAAGGCTTCCATGATGCAGTCACCTAAGACTGGGGTGTCTTAGTAGCAAGGATGACAATGTGATGTGTATTTTTGTTAACCTCTGTGTGTATGGCTTGAATTGATGCTTTGTGTGTGGCCAGAGGGGAGAGGTGGTGGTATCCTGGCACGATCGTGAAATGGATAGGATAATGTTTTTAAACTTAGTGGGAGAGAGAAATGAAAACCAACCAGAATATAAGGCCATCTAAAGTGCTAAATAGACTCAAGCAGGTTCTATGGAGGAGGAAGAAGTGATTAATTCTGATGGGGAGGCTGGGGAAGCAGGTGTCTAAGGAAAGGTTACCAAGAAGGTGGCAATTGAACTTGGCCTTGAAGGATTTAGGGGGAGAATGCTAGGGAAAATATTCCAGGGTGAGAAAATGAGTGAGAAGAGGTGCAAAAGAGGACCACTCCAGAGAAACAGTGGGTAATAAGATTTGACTGGAGGGAACATAGGTTTCATGGATATAAGCCTAGAAAAGGGACCTTGAAACCATAGAAAGCTTGAACGTCATGCTGAGGAATCTGAACTTCGTTCAGTAAGCAGAGAGCAGCCATTGAGAAATTTTAGACTAGGGATGCAATCCAGCCTTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTTTAGGGGCATGGGGGAAGGCAGGTGTTGATTATAAGTGATTTCAGTATGAAGATGAATTGAAGTAGGATTGGTCAAGTCTGTTGCCATAGTCCAGGCCAGAGAGAGTAAAGGTCTAAATTGTAGCTGGGACAGAAATTAAATGCAGAGTATTGCTATCTATGAAAGGATAGGAAGTGGACAGTAGTACATTTCCTAATAGGTACTAGTAACTTTCATGAGTCATTCATCAATATTGATTCCTTACATTGTACGGTACTACAATGTACAGGGATGAGTCAGAAATAGTCCCTGTGCTCTGAATACGTAAAAGGTTAACAAATAGGCATCAAATTACTGCATCATAATTTTAGAAATAGTCACTAATGGTGAGGAACTATAAAGGACTATGTAAAGAATATTATTTAATGGTTTGAAAAAATGTCTTACAGTGAACCTTACCGAAATAACGTGGAGTTAATAAACACTTGGAAATCATTTAAAGATATCCAGTGCAATTAATGTGGAGAAGATACCCAAATGCCAGTTTTAGGGTAGTATGGGACATTTTATGGAGTGTCCAAACCTCAGATGTCTGCGCATTTTACCTTACTATAAGGTTGTATCTTTATAGACTTTCGTGCTAATTTCTTGAGGGATAATAAAGCATATTACACTAATGCTCCAACAGTATTTGTATATTTGCAAGTGGATACAACTTTCAAGAGGGAAAATAAGCATTTTTTAAAGACCAGAATGTACCTATATTTCCACTGACCACTTCTTAAAGACTATCAAAGATAGTTTGTTCAATAAGACCTAAAGGAGAAAATATTCTTAGACTATTTCATGCTGTTAAATCTCTACAGATTTACAGTTTTATCCAGTCAAATTAATGCAAAACCCCAATGCAAGCATTTGGATTTTGAAAACTTTGGAGGAGTGTCATTCTCTAATAGTAATTATTGGTTTTACATTATTTTTTCACAGGGGAACTGATCACAGCCGCACATGAGCTTGGAGTAAGTATTAGTTTTATTGTTTAATCAATGCTCTCATTAACAGTTTTAGGAATTAAGAAAGTTTAATTAAGCATGGAGTAAAGTAGATTAATTTATTTTCAAACCCCCGTTTTTAGTAACTTATAAGTACAGTACGTGACAATTTACTTTAAGTTTTAAATCCAATTAAACTAAATTATAAAGCAAAGCCTTTACTATATATACAGTAGCTGCCTTATTATCACCCCAAATTTTGTATAAGCTGTGGGGAATAAAATAAATCGGGTTAACAGTTTTAATAAGTTTATTATTTAATAAACTTTATTATGGTGCATGATCCCTTCAGGCAAGACCTTACGACTGTCAGCATGGTGGTAATCCGATAGCAGTGTGGTCTTTCAACTTTCTAACCAATACGATATTTCAGAACCTGCTTTTTTTCAATAGCCTTTTAAATGACCCTAATGTACTGTGAACCCAGAGAACAAACTGCTTAAGAACTGACAATGAAATATGTCACCCTTTCTCTGGGTGACGCACCATGTGATAGACGCTGCCAAATCCACTAAAGAAAATATTTATTTGTATTGCCTCAAGAGGATTACAATAGAAAACCACTATTCAAACATTTAGTCATTGGTGCCTAATCTTTATAGCTGCTTGAGAAAAGGGCTACTTTTCAATTAAGGCCTGTGGGACTCTTCCTTTCCTAGATGAAAACCTTCTAACTGTTGCTAATTTTTCCGTAGGTTGCCCATCCTCCTGGCTATCCTTTGTTCACGCTGGTGGCTAAACTGGCAATTACACTGTTTCCTTTTGGTTCAATTGCCTACCGCGTCAATCTTCTCTGTGGCTTATTTGGAGCAGTAGCTGCATCATTACTTTTTTTCACCGTTTTCAGGTAAAGTAGTTGATTAGTTAAAATTAATTTTGAGCAGTTGGAGATGTAGATTTCTTATGGCTCAAGTACATACATTAAAAAAATCTTTTGTTGCTTGGTTTCCCTAACACATGTGATTTCACTTTCTTAATTTATAATACTTTCATATGCATTTGACCCCTCAAATGATTACACAGTTGGTTTTGTTTCCTACAGTGGAGTGAAGGTGTCACCAGTTCATTATCACAGTTCTCTGATTAGGCAGAACTAATGAGGTTTGTCATTTTGTGAAGATGCAGATGGGCCAGTTTAATTCAACAATATGAGGTTCATCTTTTGGTAAATGGTAAATATCATTTAATTATTCACAGTATTGCTGACGAGCAGCTGCCTATCAGGTCCAGGGCTAATACCTAATTATATTGTATTCTAAATATGAACATGTTGTATACTTTCTGAAATAAGGATATTAACTAAGGAAATCAATTTGGGATGTGGTTTTAGTAAGGTTTCACTCTGCTCCGTTATGGCTGTAGTAAAGGTAGGCAAATTAGATCCCAAGTAATTCATTGATAGAAGACTTTCTTAGGTTGGAAGTCTACCCTGCTTTTAAAACATTGGTCATTAGTTTAGAATGCTGGTAACCCATTGTCTTTGATGTTCTGTCTCCTTCATTCTTAACTCAGTGCATCCTATACCTAAGAGGATTATAGTGAAAAATACAAATTACACTTTCTGCAAAAGGAAAAACCAAATTAAAACACTTCTTCTAAAAACTTTTGCATGTCTTACTATAAAACAAATGATTTCTGTAGGTAAATATAATTTGAATAGGTACAATTTCAAATGTCTTTTTTGGAGACCAATATTTTTATTTGTGTCAAAGTCATAATACTGCCCTTTAGCCAAATTCTAAATTCTCTTTTAATTATTTATAGAAAGATAAGAGTTAGTATAATTATAACTCTGAAGTTTACTTTTGATCTGTATGTGAAAAAACTTTCAGATTCAAGTATTGTAACTGTTGATCTTTTCCCAAATTGTTATATTATTAAATTTGTTATTTTAGTCTTTATGAAATATTTAAAATAATGTTTCTGCTTAGATTCATTAGTACTATTAATATTTTTCTTTTTCTCAATGGTTAGGATAATTTTTATTAGAATTGTTCCTTCTGAGTCTTTTGTAATTAATAATCTGTCAGTATTTCCACTGAGAGAAAAAGTGTTTTT-C		Structural heart defects and renal anomalies syndrome	Pathogenic (Nov 05, 2021)
14-56585009-ATC-A			Likely pathogenic (Oct 02, 2023)
14-56585021-C-T		Inborn genetic diseases	Uncertain significance (Mar 30, 2024)
14-56585759-A-G		Structural heart defects and renal anomalies syndrome	Pathogenic (Aug 16, 2021)
14-56585773-C-G		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
14-56585805-A-T		Inborn genetic diseases	Uncertain significance (May 03, 2023)
14-56585809-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
14-56585823-TC-T		Structural heart defects and renal anomalies syndrome	Likely pathogenic (Feb 10, 2023)
14-56585829-T-C		TMEM260-related disorder	Benign (Oct 11, 2018)
14-56585836-A-G		Inborn genetic diseases	Likely benign (Feb 28, 2024)
14-56585852-A-G		Inborn genetic diseases	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM260	protein_coding	protein_coding	ENST00000261556	16	162253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.73e-19	0.0400	125612	0	136	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.741	397	358	1.11	0.0000184	4577
Missense in Polyphen		103	97.669	1.0546		1198
Synonymous	-0.774	142	131	1.09	0.00000721	1373
Loss of Function	0.962	32	38.4	0.833	0.00000192	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000950	0.000948
Ashkenazi Jewish	0.00206	0.00199
East Asian	0.000544	0.000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000540	0.000528
Middle Eastern	0.000544	0.000544
South Asian	0.000492	0.000490
Other	0.000986	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Haploinsufficiency Scores

• pHI: 0.0323
• hipred: N
• hipred_score: 0.251
• ghis: 0.533

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: Tmem260

Zebrafish Information Network

• Gene name: tmem260
• Affected structure: proximal convoluted tubule
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Cellular component: integral component of membrane