Is MIB1 p.Ser41= (c.123C>T) pathogenic?

MIB1 p.Ser41= (c.123C>T) is classified Likely benign in MIB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-07). Ultra-rare (popmax 0.0134%, amr); Associated with Inborn genetic diseases.

What condition is associated with MIB1 p.Ser41= (c.123C>T)?

MIB1 p.Ser41= (c.123C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MIB1 p.Ser41= (c.123C>T) in the general population?

MIB1 p.Ser41= (c.123C>T) is ultra-rare (popmax 0.0134%, amr) (gnomAD).

MIB1 p.Ser41=

c.123C>T · rs758651668 · VCV1757844

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, amr)

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 4.6	GERP 1.3, phastCons 1
Overall
CADD	14.92	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% Admixed American · 8/59,830 alleles

Filtering AF 0.00663% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00484%

Overall 0.000496% 8/1,611,514 alleles · ultra-rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MIB1
Protein: p.Ser41=
Coding: c.123C>T
MANE Select: NM_020774
dbSNP: rs758651668
Type: single nucleotide variant
Location: chr18:21741706 (GRCh38)
Gene constraint: LOEUF 1.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.09 · 6 PDB
Residue 41: the mib/herc2 1 domain; a β-strand

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-ser41 (accessed [today's date]).

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