CALD1

caldesmon 1

Basic information

Region (hg38): 7:134744251-134970729

Links

ENSG00000122786 ∙ NCBI:800 ∙ OMIM:114213 ∙ HGNC:1441 ∙ Uniprot:Q05682 ∙ 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 CALD1 gene.

• Inborn genetic diseases (23 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALD1 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				2		2
missense			22	4	6	32
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	7	6

Variants in CALD1

This is a list of pathogenic ClinVar variants found in the CALD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-134867753-G-A		not specified	Uncertain significance (Aug 10, 2023)
7-134928884-G-A		not specified	Uncertain significance (Mar 29, 2023)
7-134932998-G-A			Benign (Mar 05, 2018)
7-134933065-G-A		not specified	Uncertain significance (Apr 22, 2022)
7-134933128-A-C		not specified	Uncertain significance (Aug 02, 2021)
7-134933133-G-A			Likely benign (Dec 31, 2019)
7-134933148-G-A		not specified	Uncertain significance (Sep 23, 2023)
7-134933163-C-T		not specified	Uncertain significance (Dec 28, 2023)
7-134933176-G-A			Benign (Dec 31, 2019)
7-134933217-G-A		not specified	Uncertain significance (Jan 17, 2024)
7-134933245-G-A		not specified	Uncertain significance (Apr 22, 2022)
7-134933281-C-T			Benign (Dec 31, 2019)
7-134933302-G-C		not specified	Uncertain significance (Jun 21, 2022)
7-134933362-C-G		not specified	Uncertain significance (Nov 01, 2022)
7-134933502-G-C		not specified	Uncertain significance (Aug 21, 2023)
7-134933540-G-A			Likely benign (Jun 12, 2018)
7-134933614-C-T		not specified	Uncertain significance (Dec 15, 2023)
7-134933628-A-C		not specified	Uncertain significance (Jul 14, 2021)
7-134933632-T-C		not specified	Uncertain significance (Dec 19, 2023)
7-134933720-G-A			Benign (Nov 05, 2018)
7-134933722-GGGA-G			Likely benign (Dec 31, 2019)
7-134933740-C-A			Benign (Jun 26, 2017)
7-134933806-A-G		not specified	Uncertain significance (Nov 15, 2021)
7-134933849-A-G			Likely benign (Dec 31, 2019)
7-134933886-G-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALD1	protein_coding	protein_coding	ENST00000361675	13	226477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00121	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.802	387	434	0.892	0.0000251	5246
Missense in Polyphen		51	62.318	0.81838		769
Synonymous	1.52	128	152	0.843	0.00000860	1378
Loss of Function	5.46	6	46.0	0.131	0.00000269	544

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000299	0.0000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000366	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000336	0.0000327
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin- and myosin-binding protein implicated in the regulation of actomyosin interactions in smooth muscle and nonmuscle cells (could act as a bridge between myosin and actin filaments). Stimulates actin binding of tropomyosin which increases the stabilization of actin filament structure. In muscle tissues, inhibits the actomyosin ATPase by binding to F-actin. This inhibition is attenuated by calcium-calmodulin and is potentiated by tropomyosin. Interacts with actin, myosin, two molecules of tropomyosin and with calmodulin. Also play an essential role during cellular mitosis and receptor capping. Involved in Schwann cell migration during peripheral nerve regeneration (By similarity). {ECO:0000250, ECO:0000269|PubMed:8227296}.
• Pathway: Vascular smooth muscle contraction - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;Smooth Muscle Contraction;Muscle contraction;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.260

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 1.47
• rvis_percentile_EVS: 95.25

Haploinsufficiency Scores

• pHI: 0.856
• hipred: Y
• hipred_score: 0.594
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cald1
• Phenotype: muscle phenotype; growth/size/body region phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: cald1b
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: muscle contraction
• Cellular component: cytosol;cytoskeleton;plasma membrane;actin cytoskeleton;myofibril;actin cap;intracellular membrane-bounded organelle
• Molecular function: actin binding;protein binding;calmodulin binding;tropomyosin binding;myosin binding;cadherin binding