AHNAK2

AHNAK nucleoprotein 2, the group of PDZ domain containing

Basic information

Region (hg38): 14:104937243-104978374

Previous symbols: [ "C14orf78" ]

Links

ENSG00000185567 ∙ NCBI:113146 ∙ OMIM:608570 ∙ HGNC:20125 ∙ Uniprot:Q8IVF2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AR
• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AHNAK2 gene.

• Inborn genetic diseases (531 variants)
• not provided (323 variants)
• not specified (5 variants)
• Dysmetria (1 variants)
• Migraine;Hereditary episodic ataxia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHNAK2 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				135	31	166
missense			460	130	53	643
nonsense						0
start loss						0
frameshift			1	1	2	4
inframe indel				2	1	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	461	268	87

Variants in AHNAK2

This is a list of pathogenic ClinVar variants found in the AHNAK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-104938067-C-G		not specified	Uncertain significance (Oct 26, 2022)
14-104938155-A-G		not specified	Uncertain significance (Jan 03, 2024)
14-104938496-A-G		not specified	Uncertain significance (Apr 13, 2023)
14-104938518-G-A		not specified	Likely benign (Sep 20, 2023)
14-104938523-C-A		not specified	Uncertain significance (Jun 29, 2023)
14-104938547-T-C		not specified	Uncertain significance (Jan 23, 2024)
14-104938562-C-T		not specified	Likely benign (Nov 08, 2021)
14-104938592-T-C		not specified	Uncertain significance (Nov 21, 2022)
14-104938592-T-G		not specified	Uncertain significance (Aug 17, 2022)
14-104938607-G-A		not specified	Uncertain significance (Jan 23, 2023)
14-104938639-T-C			Likely benign (Mar 01, 2023)
14-104938648-G-T		not specified	Uncertain significance (Aug 30, 2021)
14-104938670-G-A		not specified	Uncertain significance (Jan 26, 2023)
14-104938705-A-G			Likely benign (Apr 01, 2022)
14-104938710-C-T		not specified	Uncertain significance (Nov 09, 2021)
14-104938733-G-T		not specified	Uncertain significance (Jan 26, 2022)
14-104938734-G-A		not specified	Uncertain significance (Oct 04, 2022)
14-104938773-C-T		not specified	Uncertain significance (Mar 07, 2024)
14-104938856-G-C		not specified	Uncertain significance (Mar 28, 2023)
14-104938906-C-T			Likely benign (Mar 01, 2024)
14-104938928-G-A		not specified	Uncertain significance (Aug 15, 2023)
14-104938950-C-T			Benign (Mar 01, 2023)
14-104939027-T-C		not specified	Uncertain significance (Apr 12, 2023)
14-104939058-C-G		not specified	Uncertain significance (Aug 02, 2022)
14-104939067-T-C		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AHNAK2	protein_coding	protein_coding	ENST00000333244	7	41114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000648	0.918	124612	0	20	124632	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-12.2	5006	3.09e+3	1.62	0.000185	37051
Missense in Polyphen		1197	758.67	1.5778		9817
Synonymous	-22.2	2382	1.35e+3	1.77	0.0000985	11684
Loss of Function	1.54	7	13.0	0.538	7.01e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.0000556	0.0000556
Finnish	0.0000497	0.0000464
European (Non-Finnish)	0.0000818	0.0000796
Middle Eastern	0.0000556	0.0000556
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 27.6
• rvis_percentile_EVS: 99.99

Haploinsufficiency Scores

• pHI: 0.0478
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0502

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ahnak2

Gene ontology

• Biological process: plasma membrane repair;regulation of RNA splicing
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;Z disc;T-tubule;cytoplasmic vesicle membrane;sarcolemma;costamere
• Molecular function: protein binding