MTSS2

MTSS I-BAR domain containing 2, the group of I-BAR domain containing

Basic information

Region (hg38): 16:70661204-70686053

Previous symbols: [ "MTSS1L" ]

Links

ENSG00000132613 ∙ NCBI:92154 ∙ OMIM:616951 ∙ HGNC:25094 ∙ Uniprot:Q765P7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder with ocular anomalies and distinctive facial features (Strong), mode of inheritance: AD
• intellectual developmental disorder with ocular anomalies and distinctive facial features (Moderate), mode of inheritance: AD
• syndromic intellectual disability (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with ocular anomalies and distinctive facial features	AD	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	Craniofacial; Neurologic; Ophthalmologic	36067766

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTSS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTSS2 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				1	1	2
missense			100	4		104
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				1	1	2
Total	0	0	104	6	2

Variants in MTSS2

This is a list of pathogenic ClinVar variants found in the MTSS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-70663691-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-70663712-C-T		not specified	Uncertain significance (May 17, 2024)
16-70663721-G-A		not specified	Uncertain significance (Nov 24, 2024)
16-70663726-C-T		not specified	Uncertain significance (Jul 09, 2021)
16-70663740-G-C		not specified	Uncertain significance (Mar 11, 2024)
16-70663752-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-70663760-C-G		not specified	Uncertain significance (Apr 09, 2024)
16-70663760-C-T		not specified	Uncertain significance (Jan 22, 2025)
16-70663765-G-A		not specified	Uncertain significance (Aug 19, 2021)
16-70663765-G-C		not specified	Uncertain significance (Apr 12, 2023)
16-70663771-T-G		not specified	Uncertain significance (Oct 29, 2021)
16-70663772-C-G		not specified	Uncertain significance (Oct 29, 2021)
16-70663774-C-G		not specified	Uncertain significance (Oct 29, 2021)
16-70663785-T-G			Likely benign (Dec 31, 2019)
16-70663786-G-A		not specified	Uncertain significance (Mar 31, 2024)
16-70663790-G-T		not specified	Uncertain significance (Sep 02, 2024)
16-70663796-T-C		not specified	Uncertain significance (Dec 15, 2024)
16-70663799-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-70663801-G-A		not specified	Uncertain significance (Sep 28, 2022)
16-70663810-G-A		not specified	Uncertain significance (Nov 08, 2024)
16-70663814-G-T		not specified	Likely benign (Nov 22, 2024)
16-70663832-T-C		not specified	Uncertain significance (Feb 22, 2025)
16-70663834-G-A		not specified	Uncertain significance (Jan 26, 2025)
16-70663840-G-A		Intellectual developmental disorder with ocular anomalies and distinctive facial features	Uncertain significance (Jul 22, 2023)
16-70663841-G-A		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTSS2	protein_coding	protein_coding	ENST00000338779	15	24863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.980	0.0200	125581	0	4	125585	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.744	427	472	0.904	0.0000320	4675
Missense in Polyphen		159	197.45	0.80525		1842
Synonymous	-3.68	288	219	1.32	0.0000166	1588
Loss of Function	4.61	5	34.0	0.147	0.00000185	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in plasma membrane dynamics. Potentiated PDGF- mediated formation of membrane ruffles and lamellipodia in fibroblasts, acting via RAC1 activation (PubMed:14752106). May function in actin bundling (PubMed:14752106). {ECO:0000269|PubMed:14752106}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.102
• rvis_EVS: -1.55
• rvis_percentile_EVS: 3.27

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.644
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.432

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtss1l
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: plasma membrane organization;cellular response to platelet-derived growth factor stimulus;activation of GTPase activity;ruffle assembly;lamellipodium organization
• Cellular component: lamellipodium;cortical actin cytoskeleton;ruffle membrane
• Molecular function: actin monomer binding;GTPase activator activity;phosphatidylinositol-4,5-bisphosphate binding;Rac GTPase binding