Is MIB1 p.Val686= (c.2058C>T) pathogenic?

MIB1 p.Val686= (c.2058C>T) is classified Likely benign in MIB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-14). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with MIB1 p.Val686= (c.2058C>T)?

MIB1 p.Val686= (c.2058C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MIB1 p.Val686= (c.2058C>T) in the general population?

MIB1 p.Val686= (c.2058C>T) is absent from gnomAD v4.1 (gnomAD).

MIB1 p.Val686=

c.2058C>T · rs2510762549 · VCV1785160

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.67	GERP -2.3, phastCons 0.017
Overall
CADD	7.012	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MIB1
Protein: p.Val686=
Coding: c.2058C>T
MANE Select: NM_020774
dbSNP: rs2510762549
Type: single nucleotide variant
Location: chr18:21844100 (GRCh38)
Gene constraint: LOEUF 1.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.09 · 6 PDB
Residue 686: an α-helix

Full MIB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MIB1 p.Ala148Ser Uncertain significance ★★ ⚠ same condition
MIB1 p.Ala570Val Uncertain significance ★★ ⚠ same condition
MIB1 p.Asn432Ser Uncertain significance ★★ ⚠ same condition
MIB1 p.Asn441Ser Uncertain significance ★★ ⚠ same condition
MIB1 p.Asn656Ser Uncertain significance ★★ ⚠ same condition
MIB1 p.Asn656Thr Uncertain significance ★★ ⚠ same condition
MIB1 p.Cys885Gly Uncertain significance ★★ ⚠ same condition
MIB1 p.Gly802Asp Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mib1-p-val686 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown