Is MBD5 p.Asp89= (c.267T>C) pathogenic?

MBD5 p.Asp89= (c.267T>C) is classified Likely benign in MBD5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-15). Ultra-rare (popmax 0.0125%, nfe); Associated with Inborn genetic diseases.

What condition is associated with MBD5 p.Asp89= (c.267T>C)?

MBD5 p.Asp89= (c.267T>C) is associated with Inborn genetic diseases, intellectual disability, autosomal dominant 1 (ClinVar).

How common is MBD5 p.Asp89= (c.267T>C) in the general population?

MBD5 p.Asp89= (c.267T>C) is ultra-rare (popmax 0.0125%, nfe) (gnomAD).

MBD5 p.Asp89=

c.267T>C · rs143333632 · VCV211437

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0125%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.86	GERP 1.2, phastCons 1
Overall
CADD	8.388	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0125% European (non-Finnish) · 148/1,179,798 alleles

Filtering AF 0.0109% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0102%

Overall 0.00942% 152/1,613,696 alleles · ultra-rare exomes 143/1,461,562 · genomes 9/152,134 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0125%	7,972
Remaining individualsnot grpmax-eligible	0.0032%	31,241
African / African-American	0.00267%	37,447

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: MBD5
Protein: p.Asp89=
Coding: c.267T>C
MANE Select: NM_001378120
dbSNP: rs143333632
Type: single nucleotide variant
Location: chr2:148463789 (GRCh38)
Gene constraint: LOEUF 0.161 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.20

Full MBD5 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

Also linked: intellectual disability, autosomal dominant 1

Similar variants

MBD5 p.Asp89Gly Uncertain significance ★ ⚠ same residue
MBD5 c.397+1G>A Pathogenic ★★ same condition
MBD5 c.397+2T>C Pathogenic ★★ same condition
MBD5 p.Arg1440Ter Pathogenic ★★ same condition
MBD5 p.Arg200Ter Pathogenic ★★ same condition
MBD5 p.Arg325Ter Pathogenic/Likely pathogenic ★★ same condition
MBD5 p.Cys60Ter Pathogenic ★★ same condition
MBD5 p.Gln587Ter Pathogenic ★★ 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/mbd5-p-asp89 (accessed [today's date]).

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