Is SMARCD2 p.Asp413= (c.1239C>T) pathogenic?

SMARCD2 p.Asp413= (c.1239C>T) is classified Likely benign in SMARCD2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-23). Rare (popmax 0.103%, amr); Associated with Inborn genetic diseases.

What condition is associated with SMARCD2 p.Asp413= (c.1239C>T)?

SMARCD2 p.Asp413= (c.1239C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SMARCD2 p.Asp413= (c.1239C>T) in the general population?

SMARCD2 p.Asp413= (c.1239C>T) is rare (popmax 0.103%, amr) (gnomAD).

SMARCD2 p.Asp413=

c.1239C>T · rs191051976 · VCV1077606

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.103%, 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 -4.4	GERP -4.6
Overall
CADD	0.229	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.103% Admixed American · 62/60,008 alleles

Filtering AF 0.0826% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0752%

Overall 0.00737% 119/1,613,912 alleles · rare exomes 96/1,461,678 · genomes 23/152,234 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.103%	968
Remaining individualsnot grpmax-eligible	0.0096%	10,414
African / African-American	0.004%	25,004
European (non-Finnish)	0.0039%	25,649
East Asian	0.00223%	44,884
South Asian	0.0011%	91,078

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: SMARCD2
Protein: p.Asp413=
Coding: c.1239C>T
MANE Select: NM_001098426
dbSNP: rs191051976
Type: single nucleotide variant
Location: chr17:63833665 (GRCh38)
Gene constraint: LOEUF 0.762 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.38

Full SMARCD2 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

SMARCD2 p.Ala434Thr Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg118Cys Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg148Gln Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg175His Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg360Cys Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg473Leu Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg476Cys Uncertain significance ★★ ⚠ same condition
SMARCD2 p.Arg494Gln 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/smarcd2-p-asp413 (accessed [today's date]).

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