Is SDHD p.Val72del (c.213_215del) pathogenic?

SDHD p.Val72del (c.213215del) is classified Likely pathogenic in SDHD (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-15). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with SDHD p.Val72del (c.213_215del)?

SDHD p.Val72del (c.213_215del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SDHD p.Val72del (c.213_215del) in the general population?

SDHD p.Val72del (c.213_215del) is no gnomAD frequency available for this variant (gnomAD).

SDHD p.Val72del

c.213_215del · rs1555186992 · VCV486442

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.2	GERP -0.53, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: SDHD
Protein: p.Val72del
Coding: c.213_215del
MANE Select: NM_003002
dbSNP: rs1555186992
Type: Deletion
Location: chr11:112088908 (GRCh38)
Gene constraint: LOEUF 0.581 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.50 · 2 PDB
Residue 72: an α-helix

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SDHD p.Val72= Benign/Likely benign ★★ same residue
SDHD p.Gln109fs Pathogenic ★★ same condition
SDHD p.Gly58fs Pathogenic ★★ same condition
SDHD p.His102fs Pathogenic/Likely pathogenic ★★ same condition
SDHD p.Leu128fs Pathogenic ★★ same condition
SDHD p.Leu20fs Pathogenic ★★ same condition
SDHD p.Pro81fs Pathogenic ★★ same condition
SDHD p.Ser132fs 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/sdhd-p-val72del (accessed [today's date]).

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