Is SDHD p.Ter160= (c.479G>A) pathogenic?

SDHD p.Ter160= (c.479G>A) is classified Benign/Likely benign in SDHD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-06-23). Very rare (popmax 0.00267%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with SDHD p.Ter160= (c.479G>A)?

SDHD p.Ter160= (c.479G>A) is associated with hereditary neoplastic syndrome, pheochromocytoma/paraganglioma syndrome 1, pheochromocytoma (ClinVar).

How common is SDHD p.Ter160= (c.479G>A) in the general population?

SDHD p.Ter160= (c.479G>A) is very rare (popmax 0.00267%, afr) (gnomAD).

SDHD p.Ter160=

c.479G>A · rs201372601 · VCV696870

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

stop-loss

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	stop-loss	predicted loss-of-function in a haploinsufficient gene (ClinGen)
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.2, phastCons 1
Overall
CADD	13.33	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,956 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000248% 4/1,610,618 alleles · very rare exomes 2/1,458,320 · genomes 2/152,298 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,478
Remaining individualsnot grpmax-eligible	0.00161%	62,272
European (non-Finnish)	8.48e-05%	1,178,706

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: SDHD
Protein: p.Ter160=
Coding: c.479G>A
MANE Select: NM_003002
dbSNP: rs201372601
Type: single nucleotide variant
Location: chr11:112094969 (GRCh38)
Gene constraint: LOEUF 0.581 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.50 · 2 PDB

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

Also linked: pheochromocytoma/paraganglioma syndrome 1 pheochromocytoma Carney-Stratakis syndrome Cowden syndrome 3 hereditary pheochromocytoma-paraganglioma

Similar variants

SDHD p.Ter160Arg Uncertain significance ★★ same residue
SDHD p.Ter160Trp Uncertain significance ★★ same residue
SDHD p.Ter160Cys Uncertain significance ★ same residue
SDHD p.Ter160Gly Uncertain significance ★ same residue
SDHD p.Ter160Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
SDHD p.Ter160Ser Uncertain significance ★ same residue
SDHD c.170-1G>T Pathogenic ★★ same condition
SDHD c.170-2A>G 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-ter160 (accessed [today's date]).

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