SYNM

synemin, the group of Intermediate filaments Type IV|A-kinase anchoring proteins

Basic information

Region (hg38): 15:99098217-99135593

Previous symbols: [ "DMN" ]

Links

ENSG00000182253

∙ NCBI:23336 ∙ OMIM:606087 ∙ HGNC:24466 ∙ Uniprot:O15061 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (117 variants)
SYNM-related_disorder (47 variants)
not_provided (43 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNM gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145728.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				21 clinvar	18 clinvar	39
missense			102 clinvar	27 clinvar	22 clinvar	151
nonsense				1 clinvar	1 clinvar	2
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	49	42

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNM	protein_coding	protein_coding	ENST00000336292	5	37379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-24	0.00348	124136	2	571	124709	0.00230

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.673	862	808	1.07	0.0000487	9932
Missense in Polyphen		212	220.73	0.96043		3031
Synonymous	-1.07	376	351	1.07	0.0000245	3219
Loss of Function	0.680	39	43.9	0.889	0.00000239	551

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0187	0.0160
Ashkenazi Jewish	0.00403	0.00398
East Asian	0.000677	0.000667
Finnish	0.00164	0.00158
European (Non-Finnish)	0.00117	0.00111
Middle Eastern	0.000677	0.000667
South Asian	0.00239	0.00236
Other	0.00233	0.00231

dbNSFP

Source: dbNSFP

Function: FUNCTION: Type-VI intermediate filament (IF) which plays an important cytoskeletal role within the muscle cell cytoskeleton. It forms heteropolymeric IFs with desmin and/or vimentin, and via its interaction with cytoskeletal proteins alpha-dystrobrevin, dystrophin, talin-1, utrophin and vinculin, is able to link these heteropolymeric IFs to adherens-type junctions, such as to the costameres, neuromuscular junctions, and myotendinous junctions within striated muscle cells. {ECO:0000269|PubMed:11353857, ECO:0000269|PubMed:16777071, ECO:0000269|PubMed:18028034}.;

Recessive Scores

pRec: 0.359

Haploinsufficiency Scores

pHI: 0.221
hipred: N
hipred_score: 0.352
ghis: 0.440

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.787

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Synm
Phenotype: growth/size/body region phenotype; muscle phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Gene ontology

Biological process: fast-twitch skeletal muscle fiber contraction;intermediate filament cytoskeleton organization
Cellular component: intermediate filament;adherens junction;sarcolemma;costamere;neurofilament cytoskeleton
Molecular function: structural constituent of cytoskeleton;protein binding;structural constituent of muscle;vinculin binding;intermediate filament binding