Is SDHA p.Ser470= (c.1410C>T) pathogenic?

SDHA p.Ser470= (c.1410C>T) is classified Benign/Likely benign in SDHA (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-26). Ultra-rare (popmax 0.0758%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with SDHA p.Ser470= (c.1410C>T)?

SDHA p.Ser470= (c.1410C>T) is associated with hereditary neoplastic syndrome, pheochromocytoma/paraganglioma syndrome 5, mitochondrial complex II deficiency, nuclear type 1 (ClinVar).

How common is SDHA p.Ser470= (c.1410C>T) in the general population?

SDHA p.Ser470= (c.1410C>T) is ultra-rare (popmax 0.0758%, sas) (gnomAD).

SDHA p.Ser470=

c.1410C>T · rs556476038 · VCV472329

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0758%, sas)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.282	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.2	GERP -2.9, phastCons 0.41
Overall
CADD	8.105	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0758% South Asian · 69/91,082 alleles

Filtering AF 0.0613% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0561%

Overall 0.00496% 80/1,614,012 alleles · ultra-rare exomes 74/1,461,662 · genomes 6/152,350 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0758%	1,320
Remaining individualsnot grpmax-eligible	0.0144%	6,943
European (non-Finnish)	0.00017%	589,936

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: SDHA
Protein: p.Ser470=
Coding: c.1410C>T
MANE Select: NM_004168
dbSNP: rs556476038
Type: single nucleotide variant
Location: chr5:236577 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 5 PDB
Residue 470: an α-helix

Full SDHA 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 5 mitochondrial complex II deficiency, nuclear type 1

Similar variants

SDHA p.Ser470Asn Uncertain significance ★★ ⚠ same residue
SDHA p.Ser470Arg Uncertain significance ★ ⚠ same residue
SDHA p.Ser470Gly Uncertain significance ★ ⚠ same residue
SDHA p.Ser470Ile Uncertain significance ★ ⚠ same residue
SDHA c.1064+1G>A Likely pathogenic ★★ same condition
SDHA c.1064+1G>T Likely pathogenic ★★ same condition
SDHA c.1064+2T>A Likely pathogenic ★★ same condition
SDHA c.1065-2A>G 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/sdha-p-ser470 (accessed [today's date]).

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