Is DSP p.Thr49= (c.147C>A) pathogenic?

DSP p.Thr49= (c.147C>A) is classified Likely benign in DSP (ClinVar, Single submitter, 1 submitter; last evaluated 2026-05-23). No allele count reported in gnomAD v4.1 (AN 1,568,266); Associated with Cardiovascular phenotype.

What condition is associated with DSP p.Thr49= (c.147C>A)?

DSP p.Thr49= (c.147C>A) is associated with Cardiovascular phenotype (ClinVar).

How common is DSP p.Thr49= (c.147C>A) in the general population?

DSP p.Thr49= (c.147C>A) is no allele count reported in gnomAD v4.1 (AN 1,568,266) (gnomAD).

DSP p.Thr49=

c.147C>A · VCV4870138

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,568,266)

Conditions

Cardiovascular phenotype

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 0.21	GERP -0.91, phastCons 0.014
Overall
CADD	9.046	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,568,266). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DSP
Protein: p.Thr49=
Coding: c.147C>A
MANE Select: NM_004415
Type: single nucleotide variant
Location: chr6:7542062 (GRCh38)
Gene constraint: LOEUF 0.443 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 49: the 'globular 1' region; the 'interaction with mapre1' region; the 'interaction with jup and pkp2' region

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DSP p.Thr49Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
DSP p.Thr49Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
DSP p.Thr49Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
DSP c.778-2A>G Likely pathogenic ★★ same condition
DSP p.Arg1267Ter Pathogenic/Likely pathogenic ★★ same condition
DSP p.Arg160Ter Pathogenic/Likely pathogenic ★★ same condition
DSP p.Arg1738Ter Pathogenic ★★ same condition
DSP p.Arg270Ter 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/dsp-p-thr49 (accessed [today's date]).

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