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): 19:44699150-44710718

Links

ENSG00000213892 ∙ NCBI:388551 ∙ OMIM:614591 ∙ HGNC:31948 ∙ Uniprot:Q2WEN9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 4B; Deafness, autosomal recessive 113	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	7655461; 21368133; 29703829

ClinVar

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

• not provided (143 variants)
• not specified (40 variants)
• Inborn genetic diseases (17 variants)
• Autosomal dominant nonsyndromic hearing loss 4B (6 variants)
• Hearing impairment (3 variants)
• Nonsyndromic genetic hearing loss (2 variants)
• Autosomal dominant nonsyndromic hearing loss 4B;Hearing loss, autosomal recessive 113 (2 variants)
• Hearing loss, autosomal recessive 113;Autosomal dominant nonsyndromic hearing loss 4B (2 variants)
• Ear malformation (1 variants)
• Hearing loss, autosomal recessive 113 (1 variants)
• Rare genetic deafness (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.

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			4	27	6	37
missense		1	67	10	3	81
nonsense	1	1				2
start loss						0
frameshift	1	1	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				3	1	4
non coding			1	15	11	27
Total	2	3	74	52	20

Highest pathogenic variant AF is 0.0000263

Variants in CEACAM16

This is a list of pathogenic ClinVar variants found in the CEACAM16 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44701028-G-T			Benign (Dec 23, 2018)
19-44701052-C-A			Benign (Nov 10, 2018)
19-44701353-C-G			Benign (Jan 11, 2021)
19-44701422-C-A			Likely benign (Aug 10, 2018)
19-44701442-G-A			Likely benign (Sep 07, 2018)
19-44701449-G-A		Autosomal dominant nonsyndromic hearing loss 4B	Uncertain significance (Nov 02, 2018)
19-44701461-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 24, 2023)
19-44701491-G-A		not specified	Uncertain significance (Aug 02, 2018)
19-44701493-G-T		Hearing loss, autosomal recessive 113	Pathogenic (Aug 03, 2021)
19-44701500-G-A		CEACAM16-related disorder	Benign/Likely benign (Oct 03, 2023)
19-44701531-C-T			Likely benign (Sep 08, 2020)
19-44703201-T-TCC			Likely benign (Dec 10, 2018)
19-44703240-C-A			Likely benign (Apr 24, 2019)
19-44703262-A-A			Benign (Jun 22, 2018)
19-44703354-T-C		not specified	Benign (Dec 20, 2023)
19-44703362-T-C		not specified	Benign (Jan 18, 2024)
19-44703372-G-A		not specified	Uncertain significance (Jan 18, 2018)
19-44703381-A-C			Uncertain significance (Aug 01, 2019)
19-44703387-C-G			Uncertain significance (Aug 10, 2022)
19-44703393-C-G			Uncertain significance (Jan 20, 2023)
19-44703402-C-A			Uncertain significance (Jun 05, 2022)
19-44703403-C-T			Uncertain significance (Sep 13, 2019)
19-44703406-G-T		not specified	Benign/Likely benign (Aug 01, 2023)
19-44703406-GC-TT		Hearing loss, autosomal recessive 113;Autosomal dominant nonsyndromic hearing loss 4B	Benign/Likely benign (Jan 19, 2024)
19-44703407-C-T		not specified	Benign/Likely benign (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEACAM16	protein_coding	protein_coding	ENST00000587331	6	11566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000158	0.875	124631	0	25	124656	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.524	253	278	0.911	0.0000193	2665
Missense in Polyphen		134	148.66	0.90141		1430
Synonymous	0.0403	129	130	0.995	0.00000950	933
Loss of Function	1.47	10	16.4	0.609	8.49e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000463	0.000436
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000118	0.000115
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000340	0.000330

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
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

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