Is MBD5 p.Asp654= (c.1962C>T) pathogenic?

MBD5 p.Asp654= (c.1962C>T) is classified Likely benign in MBD5 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-04-14). Ultra-rare (popmax 0.033%, mid); Associated with intellectual disability, autosomal dominant 1.

What condition is associated with MBD5 p.Asp654= (c.1962C>T)?

MBD5 p.Asp654= (c.1962C>T) is associated with intellectual disability, autosomal dominant 1 (ClinVar).

How common is MBD5 p.Asp654= (c.1962C>T) in the general population?

MBD5 p.Asp654= (c.1962C>T) is ultra-rare (popmax 0.033%, mid) (gnomAD).

MBD5 p.Asp654=

c.1962C>T · rs139953766 · VCV413945

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.033%, mid)

Conditions

intellectual disability, autosomal dominant 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.099	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5	GERP 2.7, phastCons 1
Overall
CADD	16.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.033% Middle Eastern · 2/6,058 alleles

Filtering AF 0.0133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0109%

Overall 0.00248% 40/1,613,938 alleles · ultra-rare exomes 32/1,461,648 · genomes 8/152,290 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.033%	3,029
African / African-American	0.0213%	4,688
South Asian	0.0121%	8,281
East Asian	0.00223%	44,876
Admixed American	0.00167%	59,994
Remaining individualsnot grpmax-eligible	0.0016%	62,488
European (non-Finnish)	0.000678%	147,487

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.Asp654=
Coding: c.1962C>T
MANE Select: NM_001378120
dbSNP: rs139953766
Type: single nucleotide variant
Location: chr2:148469905 (GRCh38)
Gene constraint: LOEUF 0.161 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.20
Residue 654: a UniProt-annotated variant site (in mrd1; uncertain significance)

Full MBD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal dominant 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MBD5 p.Asp654Glu Uncertain significance ★★ ⚠ same residue
MBD5 p.Asp654Val Likely benign ★★ ⚠ same residue
MBD5 p.Asp654Gly 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

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-asp654 (accessed [today's date]).

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