Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	117531
Gene name	Transmembrane channel like 1
Gene symbol	TMC1
Synonyms (NCBI Gene)	DFNA36DFNB11DFNB7
Chromosome	9
Chromosome location	9q21.13
Summary	This gene is considered a member of a gene family predicted to encode transmembrane proteins. The specific function of this gene is unknown; however, it is known to be required for normal function of cochlear hair cells. Mutations in this gene have been a

Show/Hide all (39)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113342704	C>A,G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, missense variant
rs121908072	G>A,C	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs121908073	C>T	Pathogenic	Coding sequence variant, stop gained
rs121908074	A>G	Pathogenic	Coding sequence variant, missense variant
rs121908076	T>C	Pathogenic	Coding sequence variant, missense variant
rs138527651	T>C	Pathogenic	Coding sequence variant, missense variant
rs151001642	C>T	Pathogenic	Stop gained, coding sequence variant
rs200171616	C>T	Pathogenic	Coding sequence variant, stop gained
rs367924428	G>A	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs370088722	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs370898981	A>G	Pathogenic-likely-pathogenic, likely-benign, pathogenic	Intron variant
rs372710475	C>T	Uncertain-significance, likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs727503483	C>A,T	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs727504554	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs730880359	->GGAGG	Pathogenic	Coding sequence variant, frameshift variant
rs747645067	T>C	Pathogenic	Missense variant, coding sequence variant
rs749491943	T>A	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs757327146	C>A,G,T	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs761261855	C>G,T	Pathogenic	Coding sequence variant, synonymous variant, missense variant
rs773851192	G>A,C	Pathogenic	Coding sequence variant, missense variant, stop gained
rs775428246	G>A,T	Likely-pathogenic, pathogenic	Splice donor variant
rs777777359	C>T	Pathogenic	Coding sequence variant, stop gained
rs786201027	T>A	Pathogenic	Coding sequence variant, missense variant
rs876657727	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs876657728	G>A	Pathogenic	Coding sequence variant, stop gained
rs876657729	G>A	Pathogenic	Coding sequence variant, stop gained
rs878853229	->A	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs878853230	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs878853240	T>C	Pathogenic	Coding sequence variant, missense variant
rs1169090943	G>A,C,T	Pathogenic	Splice donor variant, intron variant
rs1172357346	G>A,T	Likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs1554731002	G>-	Pathogenic	Splice acceptor variant
rs1564554148	A>C	Pathogenic	Splice acceptor variant
rs1564554255	G>A	Pathogenic	Stop gained, coding sequence variant
rs1564555185	->A	Pathogenic	Frameshift variant, coding sequence variant
rs1564555240	T>C	Pathogenic	Splice donor variant
rs1564556995	G>A	Pathogenic	Missense variant, coding sequence variant
rs1564583413	G>T	Pathogenic	Stop gained, coding sequence variant
rs1588067173	G>A	Likely-pathogenic	Splice donor variant

Show/Hide all (28)

miRTarBase ID	miRNA	Experiments
MIRT1427988	hsa-miR-1268	CLIP-seq
MIRT1427989	hsa-miR-1268b	CLIP-seq
MIRT1427990	hsa-miR-128	CLIP-seq
MIRT1427991	hsa-miR-1285	CLIP-seq
MIRT1427992	hsa-miR-2117	CLIP-seq
MIRT1427993	hsa-miR-3187-5p	CLIP-seq
MIRT1427994	hsa-miR-326	CLIP-seq
MIRT1427995	hsa-miR-330-5p	CLIP-seq
MIRT1427996	hsa-miR-3692	CLIP-seq
MIRT1427997	hsa-miR-378g	CLIP-seq
MIRT1427998	hsa-miR-4273	CLIP-seq
MIRT1427999	hsa-miR-4486	CLIP-seq
MIRT1428000	hsa-miR-4677-5p	CLIP-seq
MIRT1428001	hsa-miR-520f	CLIP-seq
MIRT1428002	hsa-miR-585	CLIP-seq
MIRT1428003	hsa-miR-612	CLIP-seq
MIRT1428004	hsa-miR-636	CLIP-seq
MIRT2128180	hsa-miR-1266	CLIP-seq
MIRT1427991	hsa-miR-1285	CLIP-seq
MIRT1427993	hsa-miR-3187-5p	CLIP-seq
MIRT2128181	hsa-miR-3664-3p	CLIP-seq
MIRT1427997	hsa-miR-378g	CLIP-seq
MIRT2128182	hsa-miR-4314	CLIP-seq
MIRT2128183	hsa-miR-4437	CLIP-seq
MIRT1427999	hsa-miR-4486	CLIP-seq
MIRT2128184	hsa-miR-4518	CLIP-seq
MIRT2128185	hsa-miR-4674	CLIP-seq
MIRT1428003	hsa-miR-612	CLIP-seq

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence
GO:0005245	Function	Voltage-gated calcium channel activity	IBA
GO:0005245	Function	Voltage-gated calcium channel activity	IEA
GO:0005262	Function	Calcium channel activity	IEA
GO:0005262	Function	Calcium channel activity	ISS
GO:0005886	Component	Plasma membrane	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0007605	Process	Sensory perception of sound	IEA
GO:0008381	Function	Mechanosensitive monoatomic ion channel activity	IBA
GO:0008381	Function	Mechanosensitive monoatomic ion channel activity	IEA
GO:0008381	Function	Mechanosensitive monoatomic ion channel activity	ISS
GO:0009897	Component	External side of plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0032420	Component	Stereocilium	IEA
GO:0032420	Component	Stereocilium	ISS
GO:0032426	Component	Stereocilium tip	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0050910	Process	Detection of mechanical stimulus involved in sensory perception of sound	IBA
GO:0050910	Process	Detection of mechanical stimulus involved in sensory perception of sound	IEA
GO:0060005	Process	Vestibular reflex	IBA
GO:0060005	Process	Vestibular reflex	IEA
GO:0060117	Process	Auditory receptor cell development	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:1903169	Process	Regulation of calcium ion transmembrane transport	IEA

MIM	HGNC	e!Ensembl
606706	16513	ENSG00000165091

Q8TDI8

Protein name

Transmembrane channel-like protein 1 (Transmembrane cochlear-expressed protein 1)

Protein function

Pore-forming subunit of the mechanotransducer (MET) non-selective cation channel complex located at the tips of stereocilia of cochlear hair cells and that mediates sensory transduction in the auditory system (By similarity). The MET complex is

PDB

8XOQ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF07810	TMC	515 → 630	TMC domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Detected in fetal cochlea, and at low levels in placenta and testis.

Sequence

MSPKKVQIKVEEKEDETEESSSEEEEEVEDKLPRRESLRPKRKRTRDVINEDDPEPEPED
EETRKAREKERRRRLKRGAEEEEIDEEELERLKAELDEKRQIIATVKCKPWKMEKKIEVL
KEAKKFVSENEGALGKGKGKRWFAFKMMMAKKWAKFLRDFENFKAACVPWENKIKAIESQ
FGSSVASYFLFLRWMYGVNMVLFILTFSLIMLPEYLWGLPYGSLPRKTVPRAEEASAANF
GVLYDFNGLAQYSVLFYGYYDNKRTIGWMNFRLPLSYFLVGIMCIGYSFLVVLKAMTKNI
GDDGGGDDNTFNFSWKVFTSWDYLIGNPETADNKFNSITMNFKEAITEEKAAQVEENVHL
IRFLRFLANFFVFLTLGGSGYLIFWAVKRSQEFAQQDPDTLGWWEKNEMNMVMSLLGMFC
PTLFDLFAELEDYHPLIALKWLLGRIFALLLGNLYVFILALMDEINNKIEEEKLVKANIT
LWEANMIKAYNASFSENSTGPPFFVHPADVPRGPCWETMVGQEFVRLTVSDVLTTYVTIL
IGDFLRACFVRFCNYCWCWDLEYGYPSYTEFDISGNVLALIFNQGMIWMGSFFAPSLPGI
NILRLHTSMYFQCWAVMCCNVPEARVFKASRSNNFYLGMLLLILFLSTMPVLYMIVSLPP
SFDCGPFSGKNRMFEVIGETLEHDFPSWMAKILRQLSNPGLVIAVILVMVLAIYYLNATA
KGQKAANLDLKKKMKMQALENKMRNKKMAAARAAAAAGRQ

Sequence length

760

Interactions

View interactions

337

Show/Hide Causal Diseases (12)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal dominant nonsyndromic hearing loss 36	Likely pathogenic; Pathogenic	rs747645756, rs2132189585, rs786201027, rs1448901281, rs121908072, rs121908073, rs876657727, rs138527651, rs878853229, rs777777359, rs2489958072, rs563322370, rs368084452, rs772640673, rs1289646352 View all (5 more)	RCV005040312 RCV004796651 RCV000162325 RCV005045190 RCV000004318 RCV003987310 RCV000004321 RCV001824690 RCV005049488 RCV005044467 RCV005044484 RCV003152452 RCV005047575 RCV005047629 RCV005047686 RCV005040477 RCV000626300 RCV005046846 RCV005042115 RCV001542674 RCV005042117
Autosomal recessive nonsyndromic hearing loss 7	Likely pathogenic; Pathogenic	rs1828864557, rs756960425, rs747645756, rs776689179, rs2132189585, rs1178631956, rs2118181420, rs2118284330, rs758288878, rs2489925983, rs1448901281, rs121908073, rs1169090943, rs121908076, rs876657727 View all (23 more)	RCV001328470 RCV001822894 RCV001822920 RCV006266867 RCV002051747 RCV001808902 RCV001809323 RCV001809324 RCV002444383 RCV002444384 RCV005045190 RCV000004319 RCV000004322 RCV000004323 RCV001824690 RCV000225028 RCV000225071 RCV000225099 RCV005044484 RCV003223385 RCV005047575 RCV005047629 RCV005254834 RCV005047686 RCV005040477 RCV003885394 RCV003991074 RCV000454230 RCV000770875 RCV005046846 RCV000681552 RCV000681545 RCV005042115 RCV000760983 RCV005042117 RCV000761610 RCV000760982 RCV000770876
Bilateral sensorineural hearing impairment	Pathogenic	rs747645067	RCV001027644
Deafness	Pathogenic; Likely pathogenic	rs2489883553, rs1564554255, rs773851192, rs1564555240, rs761261855	RCV004798964 RCV000679844 RCV000679842 RCV000679841 RCV000679843
Delayed speech and language development	Pathogenic	rs747645067	RCV001027644
Ear malformation	Pathogenic	rs775428246	RCV001814196
Hearing loss, autosomal recessive	Pathogenic; Likely pathogenic	rs121908073, rs121908076, rs777777359, rs775428246, rs1564554255, rs773851192, rs1564555240, rs761261855, rs757327146, rs1564556995, rs1828278868, rs1828785763, rs1290684098, rs1828965654	RCV001291357 RCV001291367 RCV001291480 RCV004719038 RCV001291359 RCV001291362 RCV001291363 RCV001291368 RCV001291361 RCV001291364 RCV001291366 RCV001291478 RCV001291479 RCV001291481
Moderate intellectual disability	Pathogenic	rs747645067	RCV001027644
Monogenic hearing loss	Likely pathogenic; Pathogenic	rs370898981	RCV006270217
Nonsyndromic genetic hearing loss	Likely pathogenic; Pathogenic	rs747645756, rs753687760, rs772640673, rs780156287, rs370898981	RCV003120624 RCV006262842 RCV004579617 RCV005063024 RCV004782031
Rare genetic deafness	Pathogenic; Likely pathogenic	rs727504554, rs730880359, rs121908072, rs121908073, rs876657727, rs876657728, rs876657729, rs138527651, rs775428246, rs151001642, rs370898981, rs370088722, rs1588067173	RCV000155718 RCV000156220 RCV000217542 RCV000211859 RCV000217598 RCV000219905 RCV000214242 RCV000221167 RCV000608719 RCV000041126 RCV000041134 RCV000041146 RCV000825547
TMC1-related disorder	Likely pathogenic; Pathogenic	rs563322370, rs2489883042, rs1207122491	RCV004534340 RCV004539018 RCV004723455

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs878853240	-
Cervical cancer	Likely benign	rs73647684	RCV005919287
Cholangiocarcinoma	Benign	rs115008515	RCV005922092
Familial cancer of breast	Benign	rs115008515	RCV005922090
Hearing impairment	Uncertain significance; Conflicting classifications of pathogenicity	rs776624164, rs1439351996, rs755694066, rs760532554	RCV001375194 RCV001526646 RCV001526647 RCV001849573
Hepatocellular carcinoma	Benign	rs200393712, rs115008515	RCV005921859 RCV005922091
Malignant tumor of esophagus	Benign	rs13285034	RCV005922077
Nonsyndromic Hearing Loss, Dominant	Uncertain significance; Benign; Likely benign	rs777589679, rs376040866	RCV000328559 RCV000344685
Sensorineural hearing loss disorder	Conflicting classifications of pathogenicity	rs1181901214	RCV005420509

Show/Hide Text Mining Associations (14)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alcoholism	Associate	26458734
Deafness	Associate	18616530, 22607986, 23226338, 23767834, 24926664, 24949729, 25388789, 26011067, 26879195, 27573290, 29434063, 29533536, 29692870, 30682115, 32802042, 33095980, 35062939, 36597107 View all (3 more)
Deafness Autosomal Recessive	Associate	24926664, 29270100
Deafness Autosomal Recessive 7	Associate	21250555, 34523024
Deafness oligodontia syndrome	Associate	21250555
Death	Associate	29270100
Hearing Disorders	Associate	39684270
Hearing Loss	Associate	18616530, 19180119, 21250555, 26079994, 26879195, 27573290, 28862181, 29196752, 29270100, 29692870, 32802042, 33205915, 33524517, 34523024, 35062939, 37582836 View all (1 more)
Hearing Loss Sensorineural	Associate	26822030, 26879195, 34795337
Hemochromatosis	Associate	29270100
Long QT Syndrome	Associate	29270100
Nonsyndromic Deafness	Associate	16134132, 19180119, 20373850, 21250555, 22607986, 23226338, 25388789, 26079994, 26822030, 28862181, 31389194, 33205915, 33524517, 34857896, 8755925
Nonsyndromic sensorineural hearing loss	Associate	16134132, 18616530, 19180119, 30733538, 34523024
Severe Acute Respiratory Syndrome	Associate	30733538

TMC1 (transmembrane channel like 1)