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.

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.

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				20	20	40
missense			47	19	22	88
nonsense				1	1	2
start loss						0
frameshift					1	1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	47	42	44

Variants in SYNM

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

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

Position	Type	Phenotype	Significance	ClinVar
15-99105224-G-A		not specified	Uncertain significance (Apr 17, 2024)
15-99105241-G-C		not specified	Uncertain significance (Sep 23, 2023)
15-99105250-G-A		SYNM-related disorder	Likely benign (May 11, 2020)
15-99105310-A-C		SYNM-related disorder	Likely benign (Feb 06, 2020)
15-99105316-G-A		SYNM-related disorder	Likely benign (Feb 21, 2020)
15-99105332-G-T		not specified	Uncertain significance (Jan 09, 2024)
15-99105335-C-T		not specified	Uncertain significance (Jun 09, 2022)
15-99105352-C-G		SYNM-related disorder	Likely benign (Sep 03, 2020)
15-99105365-G-C		not specified	Uncertain significance (Feb 22, 2023)
15-99105416-G-C		SYNM-related disorder	Likely benign (May 28, 2019)
15-99105447-G-A		not specified	Uncertain significance (May 25, 2022)
15-99105457-C-T		SYNM-related disorder	Benign (Mar 08, 2021)
15-99105468-G-A		not specified	Uncertain significance (May 28, 2024)
15-99105479-G-A		not specified	Uncertain significance (Jun 13, 2022)
15-99105481-G-C		not specified	Uncertain significance (May 27, 2022)
15-99105527-G-A		not specified	Uncertain significance (Oct 29, 2021)
15-99105529-C-T		SYNM-related disorder	Likely benign (Nov 28, 2022)
15-99105543-C-T		not specified	Uncertain significance (Jun 10, 2022)
15-99105549-A-T		not specified	Uncertain significance (Dec 02, 2021)
15-99105550-G-C		not specified	Uncertain significance (Dec 02, 2021)
15-99105561-A-C		not specified	Uncertain significance (Sep 17, 2021)
15-99105572-G-C		not specified	Uncertain significance (Dec 02, 2021)
15-99105607-G-A		SYNM-related disorder	Benign (Oct 28, 2019)
15-99105633-A-C		not specified	Uncertain significance (Sep 17, 2021)
15-99105636-C-A		not specified	Uncertain significance (Feb 05, 2024)

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_CRISPR2: N
• 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