Is HELLS p.Ser164= (c.492C>T) pathogenic?

HELLS p.Ser164= (c.492C>T) is classified Likely benign in HELLS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-08). No allele count reported in gnomAD v4.1 (AN 1,601,914).

How common is HELLS p.Ser164= (c.492C>T) in the general population?

HELLS p.Ser164= (c.492C>T) is no allele count reported in gnomAD v4.1 (AN 1,601,914) (gnomAD).

HELLS p.Ser164=

c.492C>T · VCV4778560

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 1,601,914)

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 -0.13	GERP -3.4, phastCons 0.61
Overall
CADD	4.882	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,601,914). 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: HELLS
Protein: p.Ser164=
Coding: c.492C>T
MANE Select: NM_018063
Type: single nucleotide variant
Location: chr10:94573974 (GRCh38)
Gene constraint: LOEUF 0.587 · pLI 0.63 (gnomAD)
Structure: AlphaFold pLDDT 68.76 · 4 PDB

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

Similar variants

HELLS p.Ser164Phe Uncertain significance ★ ⚠ same residue
HELLS p.Ser164Pro Uncertain significance ★ ⚠ same residue
HELLS p.Ser164_Ser165insTer Likely pathogenic ★ same residue
HELLS c.370+2T>A Pathogenic ★★ same type
HELLS c.1488+4T>C Uncertain significance ★★ same type
HELLS p.Ala16Pro Uncertain significance ★★ ⚠ same type
HELLS p.Arg319Trp Uncertain significance ★★ ⚠ same type
HELLS p.Arg507Gln Uncertain significance ★★ ⚠ same type

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/hells-p-ser164 (accessed [today's date]).

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