MAP7D1

MAP7 domain containing 1

Basic information

Region (hg38): 1:36155579-36180849

Previous symbols: [ "PARCC1", "RPRC1" ]

Links

ENSG00000116871 ∙ NCBI:55700 ∙ ∙ HGNC:25514 ∙ Uniprot:Q3KQU3 ∙ 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 MAP7D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP7D1 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			56	2	2	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	3	3

Variants in MAP7D1

This is a list of pathogenic ClinVar variants found in the MAP7D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36156421-G-A		not specified	Uncertain significance (Nov 01, 2022)
1-36156427-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-36156455-C-T		not specified	Uncertain significance (Sep 12, 2023)
1-36170986-C-T		not specified	Likely benign (Sep 01, 2021)
1-36171030-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-36171032-A-C			Likely benign (Mar 01, 2023)
1-36171153-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-36171169-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-36171173-G-A			Benign (Nov 15, 2017)
1-36171228-G-C		not specified	Uncertain significance (Mar 16, 2024)
1-36171234-C-T			Benign (Apr 10, 2018)
1-36171247-C-T		not specified	Uncertain significance (Mar 11, 2024)
1-36171271-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-36171282-G-C		not specified	Uncertain significance (Oct 20, 2023)
1-36171513-A-C		not specified	Uncertain significance (Feb 27, 2023)
1-36171558-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-36172503-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-36172515-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-36172534-G-T		not specified	Uncertain significance (Mar 11, 2022)
1-36172539-G-A		not specified	Uncertain significance (Jun 19, 2024)
1-36172545-G-A			Benign (Nov 15, 2017)
1-36172577-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-36172581-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-36172598-C-T		not specified	Uncertain significance (Jun 01, 2023)
1-36173367-C-T		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP7D1	protein_coding	protein_coding	ENST00000373151	17	25271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00801	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	449	513	0.876	0.0000351	5240
Missense in Polyphen		169	187.76	0.90011		1804
Synonymous	0.491	193	202	0.956	0.0000129	1771
Loss of Function	5.06	6	40.9	0.147	0.00000227	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000581	0.0000544
Finnish	0.0000493	0.0000462
European (Non-Finnish)	0.0000209	0.0000176
Middle Eastern	0.0000581	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.82

Haploinsufficiency Scores

• pHI: 0.0939
• hipred: N
• hipred_score: 0.436
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.607

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map7d1

Gene ontology

• Biological process: microtubule cytoskeleton organization
• Cellular component: spindle;cytosol;microtubule cytoskeleton