CEACAM16

CEA cell adhesion molecule 16, tectorial membrane component, the group of CEA cell adhesion molecule family|V-set domain containing

Basic information

Region (hg38): 19:44699151-44710718

Links

ENSG00000213892NCBI:388551OMIM:614591HGNC:31948Uniprot:Q2WEN9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • autosomal dominant nonsyndromic hearing loss 4B (Moderate), mode of inheritance: AD
  • hearing loss, autosomal recessive 113 (Strong), mode of inheritance: AR
  • autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
  • hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
  • nonsyndromic genetic hearing loss (Strong), mode of inheritance: AR
  • nonsyndromic genetic hearing loss (Moderate), mode of inheritance: AD
  • autosomal dominant nonsyndromic hearing loss 4B (Strong), mode of inheritance: AD
  • hearing loss, autosomal recessive 113 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, autosomal dominant 4B; Deafness, autosomal recessive 113AD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic7655461; 21368133; 29703829

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEACAM16 gene.

  • not_provided (192 variants)
  • Inborn_genetic_diseases (70 variants)
  • not_specified (38 variants)
  • Autosomal_dominant_nonsyndromic_hearing_loss_4B (14 variants)
  • CEACAM16-related_disorder (11 variants)
  • Hearing_loss,_autosomal_recessive_113 (9 variants)
  • Nonsyndromic_genetic_hearing_loss (3 variants)
  • Hearing_impairment (3 variants)
  • Rare_genetic_deafness (1 variants)
  • Hearing_loss,_autosomal_recessive (1 variants)
  • Ear_malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEACAM16 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039213.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
43
clinvar
3
clinvar
53
missense
4
clinvar
5
clinvar
130
clinvar
28
clinvar
2
clinvar
169
nonsense
3
clinvar
4
clinvar
7
start loss
0
frameshift
2
clinvar
2
clinvar
1
clinvar
5
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total 10 11 139 71 5

Highest pathogenic variant AF is 0.0000558823

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CEACAM16protein_codingprotein_codingENST00000587331 611566
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001580.8751246310251246560.000100
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5242532780.9110.00001932665
Missense in Polyphen134148.660.901411430
Synonymous0.04031291300.9950.00000950933
Loss of Function1.471016.40.6098.49e-7172

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004630.000436
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001180.000115
Middle Eastern0.000.00
South Asian0.000.00
Other0.0003400.000330

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for proper hearing, it may play a role in maintaining the integrity of the tectorial membrane. {ECO:0000269|PubMed:21368133, ECO:0000269|PubMed:25589040}.;
Disease
DISEASE: Deafness, autosomal dominant, 4B (DFNA4B) [MIM:614614]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:21368133, ECO:0000269|PubMed:25589040}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Intolerance Scores

loftool
0.498
rvis_EVS
-0.4
rvis_percentile_EVS
26.85

Haploinsufficiency Scores

pHI
0.111
hipred
N
hipred_score
0.234
ghis
0.403

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.231

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ceacam16
Phenotype
vision/eye phenotype; hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process
sensory perception of sound
Cellular component
extracellular space;stereocilium tip
Molecular function
identical protein binding